Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-07 23:55 -0500 (Sat, 07 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4888
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4678
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/31HostnameOS / ArchCHECK
biodbNcbi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-02-07 09:55 -0500 (Sat, 07 Feb 2026)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: RELEASE_3_22
git_last_commit: dc1f90a
git_last_commit_date: 2025-10-29 11:15:40 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on merida1

To the developers/maintainers of the biodbNcbi package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbNcbi
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
StartedAt: 2026-02-07 16:01:18 -0500 (Sat, 07 Feb 2026)
EndedAt: 2026-02-07 16:02:34 -0500 (Sat, 07 Feb 2026)
EllapsedTime: 76.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2026-02-07 16:02:22.076][biodb::testContext]
biodb.INFO [2026-02-07 16:02:22.079][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:22.080][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2026-02-07 16:02:22.082][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:22.083][biodb::testContext]
biodb.INFO [2026-02-07 16:02:22.089][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:22.091][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:22.099][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:22.100][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-07 16:02:22.102][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-07 16:02:22.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.106][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-07 16:02:22.131][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-07 16:02:22.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.136][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-07 16:02:22.137][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-07 16:02:22.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.142][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-07 16:02:22.143][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-07 16:02:22.144][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-07 16:02:22.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.149][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-07 16:02:22.151][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-07 16:02:22.152][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-07 16:02:22.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.156][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-07 16:02:22.158][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-07 16:02:22.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.162][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-07 16:02:22.164][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-07 16:02:22.165][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-07 16:02:22.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.169][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-07 16:02:22.171][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-07 16:02:22.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.175][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-07 16:02:22.177][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-07 16:02:22.178][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-07 16:02:22.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.182][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:22.184][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-07 16:02:22.185][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-07 16:02:22.186][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-07 16:02:22.188][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-07 16:02:22.189][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-07 16:02:22.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.194][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-07 16:02:22.195][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-07 16:02:22.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.200][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-07 16:02:22.201][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-07 16:02:22.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.206][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-07 16:02:22.207][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-07 16:02:22.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.211][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-07 16:02:22.213][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-07 16:02:22.214][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-07 16:02:22.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.219][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:22.220][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-07 16:02:22.231][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-07 16:02:22.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.235][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-07 16:02:22.237][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-07 16:02:22.238][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-07 16:02:22.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.245][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-07 16:02:22.297][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.319][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-07 16:02:22.320][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.322][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:22.323][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.324][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.325][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.327][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.328][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:22.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:22.330][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.332][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-07 16:02:22.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:22.334][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.336][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.337][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:22.337][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:22.337][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:22.337][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:22.337][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:22.338][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:22.339][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.341][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.342][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:22.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.345][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.347][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.348][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:22.349][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:22.350][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.352][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.353][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-07 16:02:22.355][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.357][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:22.358][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.359][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:22.360][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.362][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.363][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.364][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.365][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:22.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:22.368][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.369][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-07 16:02:22.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:22.372][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.373][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.374][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:22.374][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:22.374][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:22.374][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:22.374][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:22.376][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:22.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.379][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:22.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.383][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.384][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:22.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:22.388][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.389][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.390][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-07 16:02:22.392][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.394][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-07 16:02:22.395][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:22.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.399][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.400][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.401][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.402][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:22.404][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:22.405][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.406][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-07 16:02:22.408][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:22.409][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.410][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.411][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.413][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:22.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.416][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:22.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.421][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.422][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:22.423][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:22.424][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.426][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.427][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-07 16:02:22.429][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.431][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:22.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:22.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.436][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.437][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.438][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.439][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:22.441][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:22.442][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.443][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-07 16:02:22.445][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:22.446][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.447][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.448][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.450][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:22.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.453][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:22.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.457][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.458][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.459][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:22.461][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:22.462][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.463][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.467][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:22.468][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.566][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-07 16:02:22.571][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-07 16:02:22.572][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-07 16:02:22.574][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-07 16:02:22.576][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-07 16:02:22.578][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-07 16:02:22.579][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:22.581][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:22.583][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-07 16:02:22.584][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-07 16:02:22.586][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-07 16:02:22.588][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-07 16:02:22.590][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:22.591][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:22.593][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:22.595][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:22.597][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-07 16:02:22.598][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-07 16:02:22.600][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-07 16:02:22.602][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-07 16:02:22.604][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-07 16:02:22.605][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-07 16:02:22.607][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-07 16:02:22.609][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-07 16:02:22.611][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-07 16:02:22.612][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-07 16:02:22.614][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-07 16:02:22.616][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-07 16:02:22.618][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-07 16:02:22.619][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-07 16:02:22.621][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-07 16:02:22.623][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-07 16:02:22.625][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-07 16:02:22.626][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-07 16:02:22.628][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-07 16:02:22.630][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-07 16:02:22.631][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-07 16:02:22.633][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-07 16:02:22.635][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-07 16:02:22.637][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-07 16:02:22.638][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-07 16:02:22.640][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-07 16:02:22.642][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-07 16:02:22.644][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-07 16:02:22.645][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-07 16:02:22.647][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:22.649][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-07 16:02:22.651][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-07 16:02:22.652][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-07 16:02:22.654][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-07 16:02:22.656][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-07 16:02:22.657][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-07 16:02:22.659][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-07 16:02:22.661][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-07 16:02:22.663][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-07 16:02:22.664][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-07 16:02:22.666][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-07 16:02:22.668][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-07 16:02:22.670][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-07 16:02:22.671][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-07 16:02:22.673][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-07 16:02:22.675][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-07 16:02:22.677][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-07 16:02:22.678][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-07 16:02:22.680][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-07 16:02:22.682][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-07 16:02:22.683][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-07 16:02:22.685][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-07 16:02:22.687][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-07 16:02:22.689][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-07 16:02:22.690][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-07 16:02:22.692][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-07 16:02:22.694][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-07 16:02:22.696][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-07 16:02:22.697][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-07 16:02:22.699][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-07 16:02:22.701][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-07 16:02:22.703][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-07 16:02:22.705][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-07 16:02:22.706][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-07 16:02:22.708][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-07 16:02:22.710][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-07 16:02:22.712][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-07 16:02:22.720][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-07 16:02:22.722][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:22.725][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:22.726][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.729][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:22.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:22.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:22.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:22.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:22.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:22.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:22.866][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:22.879][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-07 16:02:22.882][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.883][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-07 16:02:22.884][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.886][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:22.887][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.888][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.889][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.891][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.892][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-07 16:02:22.893][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:22.894][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.896][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-07 16:02:22.897][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:22.898][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-07 16:02:22.898][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-07 16:02:22.899][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.901][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.902][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:22.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.905][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:22.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.910][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-07 16:02:22.910][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-07 16:02:22.911][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:22.912][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:22.914][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.915][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.916][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-07 16:02:22.919][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.920][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-07 16:02:22.921][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.922][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:22.924][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.925][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.926][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.927][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.929][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:22.930][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:22.931][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.932][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-07 16:02:22.934][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:22.935][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-07 16:02:22.935][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-07 16:02:22.935][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-07 16:02:22.935][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-07 16:02:22.935][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-07 16:02:22.935][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-07 16:02:22.936][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.937][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:22.939][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:22.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.942][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:22.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.946][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.947][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:22.947][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:22.948][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:22.949][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:22.950][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.952][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:22.953][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-07 16:02:22.955][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.957][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-07 16:02:22.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:22.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.962][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.963][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.965][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:22.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:22.968][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.969][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-07 16:02:22.970][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.972][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:22.973][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:22.974][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:22.974][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:22.974][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:22.976][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-07 16:02:22.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.979][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:22.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:22.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:22.983][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:22.984][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:22.984][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:22.984][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-07 16:02:22.985][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:22.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:22.988][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.989][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-07 16:02:22.990][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-07 16:02:22.993][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.994][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-07 16:02:22.995][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.997][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:22.998][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:22.999][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:23.000][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:23.002][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:23.003][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:23.004][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:23.006][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:23.007][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-07 16:02:23.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:23.009][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-07 16:02:23.009][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-07 16:02:23.011][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:23.012][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:23.013][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-07 16:02:23.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:23.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:23.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:23.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:23.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:23.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:23.022][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:23.022][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:23.022][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-07 16:02:23.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:23.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:23.025][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:23.026][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-07 16:02:23.034][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-07 16:02:23.036][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:23.039][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:23.041][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-07 16:02:23.042][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:23.044][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-07 16:02:23.071][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-02-07 16:02:23.086][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2026-02-07 16:02:23.095][biodb::testThat]
biodb.INFO [2026-02-07 16:02:23.097][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-07 16:02:23.098][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:23.099][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:23.104][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2026-02-07 16:02:23.106][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:23.109][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-02-07 16:02:23.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:23.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:23.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:23.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:23.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:23.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:23.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:23.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.181][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:23.198][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.200][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.201][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.237][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:23.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.243][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.248][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.258][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:23.350][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2026-02-07 16:02:23.353][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.358][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.395][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:23.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:23.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.400][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:23.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:23.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.405][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:23.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:23.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.410][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:23.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:23.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.438][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.481][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.491][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.520][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.521][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.523][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.524][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.546][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:23.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.551][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.556][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.561][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:23.563][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.564][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.565][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.566][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:23.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.582][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.583][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.585][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.586][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.592][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.593][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.595][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.596][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.619][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2026-02-07 16:02:23.667][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:23.668][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-02-07 16:02:23.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:23.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:23.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:23.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:23.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:23.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:23.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:23.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.725][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:23.727][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.728][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.729][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.731][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:23.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.736][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.741][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.787][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:23.821][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2026-02-07 16:02:23.849][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.854][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:23.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.859][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:23.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:23.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.864][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:23.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:23.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.869][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:23.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:23.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.874][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:23.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:23.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.890][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.933][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.938][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:23.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.985][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.986][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.992][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.993][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:23.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:23.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:23.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:23.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:24.010][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:24.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:24.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:24.015][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:24.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:24.020][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:24.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:24.025][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:24.026][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:24.029][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:24.030][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-07 16:02:24.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:24.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:24.046][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.047][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:24.048][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:24.050][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:24.056][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:24.058][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:24.059][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:24.060][ef$get] fields variable is a list.
biodb.INFO [2026-02-07 16:02:24.071][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.073][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-07 16:02:24.074][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:24.075][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:24.078][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2026-02-07 16:02:24.083][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2026-02-07 16:02:24.087][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-07 16:02:24.089][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:24.090][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-07 16:02:24.092][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:24.093][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-07 16:02:24.280][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.281][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-07 16:02:24.282][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:24.284][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.292][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.293][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-07 16:02:24.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:24.295][biodb::testThat]
biodb.WARN [2026-02-07 16:02:24.317][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-07 16:02:24.342][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-07 16:02:24.353][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.355][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-07 16:02:24.356][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:24.357][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:24.381][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2026-02-07 16:02:24.453][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:24.494][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-07 16:02:24.496][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:24.497][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-07 16:02:24.498][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:24.500][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-07 16:02:24.635][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.637][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-07 16:02:24.638][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:24.639][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-07 16:02:24.698][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.700][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-07 16:02:24.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:24.702][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.712][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.714][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:24.715][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:24.716][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-07 16:02:24.776][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.777][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:24.778][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:24.779][biodb::testThat]
biodb.INFO [2026-02-07 16:02:24.788][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-07 16:02:24.790][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-02-07 16:02:24.791][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-07 16:02:24.792][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:24.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:24.794][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:24.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:24.796][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-07 16:02:24.815][biodb::testContext]
biodb.INFO [2026-02-07 16:02:24.816][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:24.818][biodb::testContext] Test context - Gene long tests
biodb.INFO [2026-02-07 16:02:24.819][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:24.820][biodb::testContext]
biodb.INFO [2026-02-07 16:02:24.822][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:24.824][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:24.829][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:24.830][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-07 16:02:24.831][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-07 16:02:24.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.836][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-07 16:02:24.838][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-07 16:02:24.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.842][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-07 16:02:24.844][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-07 16:02:24.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.848][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-07 16:02:24.850][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-07 16:02:24.851][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-07 16:02:24.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.856][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-07 16:02:24.857][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-07 16:02:24.858][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-07 16:02:24.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.863][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-07 16:02:24.864][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-07 16:02:24.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.869][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-07 16:02:24.870][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-07 16:02:24.872][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-07 16:02:24.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.876][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-07 16:02:24.878][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-07 16:02:24.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.882][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-07 16:02:24.884][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-07 16:02:24.885][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-07 16:02:24.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.890][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:24.891][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-07 16:02:24.892][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-07 16:02:24.893][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-07 16:02:24.895][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-07 16:02:24.896][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-07 16:02:24.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.901][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-07 16:02:24.902][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-07 16:02:24.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.907][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-07 16:02:24.908][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-07 16:02:24.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.913][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-07 16:02:24.914][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-07 16:02:24.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.918][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-07 16:02:24.920][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-07 16:02:24.921][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-07 16:02:24.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.926][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:24.927][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-07 16:02:24.938][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-07 16:02:24.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.943][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-07 16:02:24.944][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-07 16:02:24.945][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-07 16:02:24.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:24.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:24.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:24.951][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-07 16:02:24.953][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:24.954][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-07 16:02:24.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:24.957][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:24.958][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:24.959][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:24.961][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:24.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:24.963][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:24.964][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:24.966][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:24.967][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-07 16:02:24.968][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:24.970][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:24.971][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:24.972][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:24.972][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:24.972][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:24.972][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:24.972][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:24.974][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:24.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:24.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:24.977][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:24.978][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:24.980][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:24.981][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:24.982][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:24.983][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:24.984][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:24.986][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:24.987][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:24.989][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-07 16:02:24.991][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:24.992][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:24.993][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:24.994][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:24.996][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:24.997][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:24.998][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:24.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.001][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:25.002][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:25.003][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.005][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-07 16:02:25.006][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:25.007][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.008][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.014][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:25.014][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:25.014][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:25.014][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:25.014][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:25.016][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:25.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.019][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:25.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.024][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:25.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:25.028][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.029][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.030][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-07 16:02:25.032][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.034][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-07 16:02:25.035][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.036][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:25.038][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.039][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.040][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.041][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.043][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:25.044][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:25.045][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.046][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-07 16:02:25.048][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:25.049][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.050][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.051][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.053][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:25.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.056][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:25.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.060][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.061][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.062][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:25.063][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:25.065][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.066][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.067][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-07 16:02:25.069][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.071][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:25.072][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.073][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:25.074][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.076][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.077][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.078][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.079][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:25.081][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:25.082][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.083][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-07 16:02:25.085][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:25.086][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.087][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.088][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.090][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:25.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:25.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.097][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.098][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.099][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:25.101][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:25.102][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.103][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.105][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:25.106][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.201][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-07 16:02:25.203][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-07 16:02:25.205][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-07 16:02:25.207][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-07 16:02:25.213][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-07 16:02:25.214][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-07 16:02:25.216][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:25.218][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:25.219][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-07 16:02:25.221][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-07 16:02:25.223][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-07 16:02:25.224][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-07 16:02:25.226][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:25.228][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:25.229][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:25.231][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:25.233][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-07 16:02:25.235][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-07 16:02:25.236][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-07 16:02:25.238][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-07 16:02:25.240][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-07 16:02:25.242][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-07 16:02:25.243][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-07 16:02:25.245][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-07 16:02:25.247][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-07 16:02:25.248][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-07 16:02:25.250][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-07 16:02:25.252][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-07 16:02:25.254][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-07 16:02:25.255][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-07 16:02:25.257][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-07 16:02:25.259][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-07 16:02:25.261][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-07 16:02:25.262][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-07 16:02:25.264][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-07 16:02:25.266][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-07 16:02:25.267][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-07 16:02:25.269][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-07 16:02:25.271][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-07 16:02:25.272][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-07 16:02:25.274][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-07 16:02:25.276][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-07 16:02:25.278][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-07 16:02:25.279][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-07 16:02:25.281][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-07 16:02:25.283][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:25.285][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-07 16:02:25.287][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-07 16:02:25.288][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-07 16:02:25.290][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-07 16:02:25.292][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-07 16:02:25.294][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-07 16:02:25.295][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-07 16:02:25.297][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-07 16:02:25.299][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-07 16:02:25.301][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-07 16:02:25.302][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-07 16:02:25.304][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-07 16:02:25.306][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-07 16:02:25.308][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-07 16:02:25.310][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-07 16:02:25.312][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-07 16:02:25.314][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-07 16:02:25.316][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-07 16:02:25.318][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-07 16:02:25.320][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-07 16:02:25.323][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-07 16:02:25.325][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-07 16:02:25.327][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-07 16:02:25.329][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-07 16:02:25.330][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-07 16:02:25.332][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-07 16:02:25.334][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-07 16:02:25.336][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-07 16:02:25.338][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-07 16:02:25.340][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-07 16:02:25.342][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-07 16:02:25.344][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-07 16:02:25.347][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-07 16:02:25.349][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-07 16:02:25.351][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-07 16:02:25.353][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-07 16:02:25.355][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-07 16:02:25.357][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-07 16:02:25.359][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:25.361][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:25.362][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.364][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:25.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:25.503][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:25.505][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-07 16:02:25.507][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.509][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-07 16:02:25.510][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.511][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:25.513][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.514][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.515][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.517][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.518][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-07 16:02:25.519][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:25.522][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.524][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-07 16:02:25.525][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:25.527][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-07 16:02:25.527][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-07 16:02:25.528][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.529][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.530][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:25.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.534][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:25.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.538][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.539][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-07 16:02:25.539][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-07 16:02:25.540][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:25.541][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:25.543][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.544][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.545][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-07 16:02:25.548][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.549][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-07 16:02:25.550][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.552][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:25.553][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.554][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.555][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.557][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.558][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:25.559][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:25.561][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.562][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-07 16:02:25.563][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:25.564][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-07 16:02:25.564][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-07 16:02:25.564][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-07 16:02:25.564][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-07 16:02:25.564][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-07 16:02:25.564][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-07 16:02:25.566][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.567][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:25.568][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:25.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.572][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:25.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.575][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.576][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.577][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:25.577][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:25.579][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:25.580][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:25.581][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.582][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.584][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-07 16:02:25.586][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.588][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-07 16:02:25.589][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.590][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:25.591][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.593][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.594][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.595][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.596][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:25.598][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:25.599][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.600][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-07 16:02:25.602][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.603][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:25.604][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.606][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:25.606][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:25.606][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:25.611][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-07 16:02:25.612][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.613][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.615][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:25.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.617][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.618][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.619][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:25.619][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:25.619][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-07 16:02:25.621][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:25.622][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:25.623][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.624][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-07 16:02:25.626][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-07 16:02:25.628][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.629][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-07 16:02:25.631][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.632][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:25.633][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.636][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.637][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.638][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:25.639][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:25.641][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.642][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-07 16:02:25.643][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:25.644][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-07 16:02:25.644][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-07 16:02:25.646][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:25.647][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:25.648][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-07 16:02:25.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.652][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:25.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:25.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:25.655][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:25.657][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:25.657][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:25.657][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-07 16:02:25.658][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:25.659][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:25.660][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:25.661][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-07 16:02:25.663][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-07 16:02:25.665][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:25.667][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:25.669][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-07 16:02:25.671][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:25.672][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-07 16:02:25.681][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2026-02-07 16:02:25.723][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2026-02-07 16:02:25.729][biodb::testThat]
biodb.INFO [2026-02-07 16:02:25.731][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-07 16:02:25.734][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:25.735][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:25.743][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2026-02-07 16:02:25.744][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:25.750][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2026-02-07 16:02:25.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:25.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:25.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:25.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:25.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:25.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:25.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:25.778][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.780][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.781][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.782][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.789][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:25.791][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:25.792][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.793][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.795][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:25.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:25.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.800][ef$get] Asked field names are: location.
biodb.TRACE[2026-02-07 16:02:25.801][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-02-07 16:02:25.803][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.804][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.806][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2026-02-07 16:02:25.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-02-07 16:02:25.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.811][ef$get] Asked field names are: symbol.
biodb.TRACE[2026-02-07 16:02:25.812][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-02-07 16:02:25.814][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.815][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.817][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2026-02-07 16:02:25.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-02-07 16:02:25.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.822][ef$get] Asked field names are: synonyms.
biodb.TRACE[2026-02-07 16:02:25.823][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:25.830][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.832][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.834][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2026-02-07 16:02:25.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:25.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.839][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-02-07 16:02:25.841][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-02-07 16:02:25.842][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.843][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.846][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-02-07 16:02:25.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-02-07 16:02:25.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.856][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:25.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:25.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.862][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-07 16:02:25.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-07 16:02:25.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.867][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-07 16:02:25.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-07 16:02:25.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.878][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-07 16:02:25.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-07 16:02:25.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:25.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:25.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:25.915][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2026-02-07 16:02:25.917][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:25.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:25.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.923][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:25.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:25.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.928][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:25.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:25.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.934][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:25.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:25.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:25.939][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:25.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:25.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:25.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:25.944][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2026-02-07 16:02:25.986][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-02-07 16:02:26.006][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2026-02-07 16:02:26.007][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2026-02-07 16:02:26.012][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:26.013][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-07 16:02:26.015][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:26.021][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-07 16:02:26.022][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:26.024][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-07 16:02:26.085][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.086][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-07 16:02:26.087][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:26.088][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:26.091][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2026-02-07 16:02:26.093][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2026-02-07 16:02:26.095][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-07 16:02:26.096][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:26.098][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:26.099][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:26.100][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:26.101][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-07 16:02:26.161][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.163][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-07 16:02:26.164][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:26.165][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:26.169][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:26.171][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:26.172][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:26.173][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:26.175][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2026-02-07 16:02:26.186][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-07 16:02:26.188][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:26.190][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-07 16:02:26.191][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:26.196][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:26.198][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:26.199][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:26.223][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-07 16:02:26.301][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.303][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-07 16:02:26.304][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:26.305][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:26.315][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-07 16:02:26.317][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:26.319][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-07 16:02:26.320][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:26.321][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:26.322][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:26.324][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:26.325][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-07 16:02:26.388][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.389][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-07 16:02:26.390][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:26.392][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:26.397][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-07 16:02:26.398][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:26.400][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-07 16:02:26.402][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:26.403][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:26.404][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:26.406][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:26.407][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-07 16:02:26.517][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.519][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-07 16:02:26.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:26.524][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-07 16:02:26.616][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.617][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-07 16:02:26.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:26.619][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.630][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.631][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:26.632][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:26.633][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-07 16:02:26.694][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.695][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:26.697][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:26.698][biodb::testThat]
biodb.INFO [2026-02-07 16:02:26.707][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-07 16:02:26.708][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2026-02-07 16:02:26.709][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-02-07 16:02:26.711][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-07 16:02:26.712][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:26.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:26.714][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:26.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:26.716][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-07 16:02:26.722][biodb::testContext]
biodb.INFO [2026-02-07 16:02:26.724][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:26.725][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2026-02-07 16:02:26.726][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:26.727][biodb::testContext]
biodb.INFO [2026-02-07 16:02:26.730][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:26.732][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:26.736][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:26.737][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-07 16:02:26.739][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-07 16:02:26.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.743][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-07 16:02:26.745][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-07 16:02:26.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.749][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-07 16:02:26.751][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-07 16:02:26.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.755][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-07 16:02:26.757][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-07 16:02:26.758][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-07 16:02:26.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.763][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-07 16:02:26.764][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-07 16:02:26.765][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-07 16:02:26.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.770][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-07 16:02:26.771][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-07 16:02:26.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.776][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-07 16:02:26.777][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-07 16:02:26.778][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-07 16:02:26.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.783][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-07 16:02:26.784][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-07 16:02:26.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.789][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-07 16:02:26.790][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-07 16:02:26.792][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-07 16:02:26.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.801][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:26.802][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-07 16:02:26.804][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-07 16:02:26.805][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-07 16:02:26.806][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-07 16:02:26.807][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-07 16:02:26.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.812][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-07 16:02:26.813][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-07 16:02:26.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.818][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-07 16:02:26.819][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-07 16:02:26.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.824][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-07 16:02:26.825][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-07 16:02:26.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.830][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-07 16:02:26.831][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-07 16:02:26.833][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-07 16:02:26.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.837][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:26.839][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-07 16:02:26.849][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-07 16:02:26.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.854][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-07 16:02:26.856][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-07 16:02:26.857][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-07 16:02:26.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:26.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:26.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:26.862][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-07 16:02:26.864][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.865][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-07 16:02:26.866][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.868][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:26.869][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.870][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.872][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.873][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.874][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:26.875][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:26.877][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.878][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-07 16:02:26.879][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:26.881][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.882][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.883][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:26.883][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:26.883][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:26.883][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:26.883][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:26.885][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:26.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:26.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:26.888][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:26.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:26.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:26.892][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.893][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.894][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:26.896][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:26.897][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.898][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.900][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-07 16:02:26.902][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.903][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:26.904][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.906][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:26.907][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.908][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.909][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.911][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.912][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:26.913][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:26.914][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.916][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-07 16:02:26.917][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:26.918][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.920][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.921][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:26.921][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:26.921][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:26.921][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:26.921][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:26.922][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:26.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:26.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:26.926][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:26.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:26.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:26.929][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.930][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.932][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:26.933][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:26.934][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.935][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.937][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-07 16:02:26.939][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.940][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-07 16:02:26.942][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.943][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:26.944][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.945][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.947][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.948][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.949][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:26.950][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:26.952][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.953][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-07 16:02:26.954][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:26.955][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.957][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.958][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.959][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:26.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:26.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:26.963][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:26.964][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:26.965][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:26.966][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.968][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.969][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:26.970][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:26.971][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.973][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:26.974][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-07 16:02:26.977][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.978][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:26.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.981][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:26.982][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:26.983][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.985][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.986][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:26.987][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:26.993][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:26.995][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:26.996][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-07 16:02:26.997][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:26.999][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:27.000][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.001][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:27.002][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:27.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.006][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:27.007][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.009][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.011][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:27.012][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:27.013][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:27.014][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:27.016][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:27.017][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:27.018][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.111][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-07 16:02:27.112][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-07 16:02:27.114][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-07 16:02:27.116][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-07 16:02:27.118][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-07 16:02:27.119][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-07 16:02:27.121][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:27.123][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:27.125][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-07 16:02:27.126][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-07 16:02:27.128][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-07 16:02:27.130][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-07 16:02:27.131][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:27.133][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:27.135][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:27.137][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:27.138][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-07 16:02:27.140][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-07 16:02:27.142][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-07 16:02:27.144][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-07 16:02:27.145][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-07 16:02:27.147][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-07 16:02:27.149][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-07 16:02:27.150][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-07 16:02:27.152][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-07 16:02:27.154][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-07 16:02:27.156][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-07 16:02:27.157][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-07 16:02:27.159][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-07 16:02:27.161][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-07 16:02:27.163][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-07 16:02:27.164][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-07 16:02:27.170][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-07 16:02:27.172][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-07 16:02:27.174][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-07 16:02:27.176][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-07 16:02:27.178][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-07 16:02:27.180][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-07 16:02:27.183][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-07 16:02:27.185][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-07 16:02:27.187][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-07 16:02:27.190][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-07 16:02:27.194][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-07 16:02:27.199][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-07 16:02:27.213][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-07 16:02:27.219][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:27.223][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-07 16:02:27.229][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-07 16:02:27.262][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-07 16:02:27.271][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-07 16:02:27.274][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-07 16:02:27.288][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-07 16:02:27.291][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-07 16:02:27.295][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-07 16:02:27.298][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-07 16:02:27.302][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-07 16:02:27.305][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-07 16:02:27.308][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-07 16:02:27.311][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-07 16:02:27.314][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-07 16:02:27.317][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-07 16:02:27.321][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-07 16:02:27.324][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-07 16:02:27.328][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-07 16:02:27.331][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-07 16:02:27.335][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-07 16:02:27.338][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-07 16:02:27.342][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-07 16:02:27.345][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-07 16:02:27.349][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-07 16:02:27.353][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-07 16:02:27.357][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-07 16:02:27.360][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-07 16:02:27.364][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-07 16:02:27.367][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-07 16:02:27.370][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-07 16:02:27.373][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-07 16:02:27.377][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-07 16:02:27.380][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-07 16:02:27.384][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-07 16:02:27.388][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-07 16:02:27.391][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-07 16:02:27.395][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-07 16:02:27.398][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-07 16:02:27.402][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:27.404][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:27.407][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.411][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:27.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:27.625][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:27.627][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-07 16:02:27.630][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.631][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-07 16:02:27.632][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.634][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:27.635][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.636][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.637][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.640][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-07 16:02:27.641][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:27.642][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.644][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-07 16:02:27.645][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:27.646][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-07 16:02:27.646][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-07 16:02:27.648][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:27.649][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:27.650][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:27.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.654][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:27.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.657][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.658][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-07 16:02:27.658][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-07 16:02:27.660][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:27.661][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:27.662][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.663][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:27.665][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-07 16:02:27.667][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.669][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-07 16:02:27.670][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.671][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:27.672][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.674][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.675][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.676][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.677][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:27.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:27.680][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.681][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-07 16:02:27.682][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:27.684][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-07 16:02:27.684][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-07 16:02:27.684][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-07 16:02:27.684][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-07 16:02:27.684][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-07 16:02:27.684][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-07 16:02:27.685][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:27.686][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:27.687][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:27.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:27.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.695][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.696][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:27.696][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:27.697][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:27.698][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:27.699][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.701][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:27.702][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-07 16:02:27.705][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:27.706][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-07 16:02:27.707][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.708][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:27.710][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.711][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.712][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.713][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.715][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:27.716][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:27.717][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.718][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-07 16:02:27.720][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.721][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:27.722][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:27.724][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:27.724][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:27.724][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:27.725][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-07 16:02:27.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.728][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:27.730][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.731][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.732][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.733][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:27.733][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:27.733][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-07 16:02:27.735][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:27.736][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:27.737][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.738][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-07 16:02:27.740][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-07 16:02:27.742][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.743][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-07 16:02:27.745][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.746][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:27.747][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.753][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.754][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.755][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.756][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:27.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:27.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.760][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-07 16:02:27.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:27.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-07 16:02:27.763][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-07 16:02:27.764][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:27.765][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:27.767][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-07 16:02:27.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.770][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:27.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:27.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:27.774][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:27.775][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:27.775][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:27.775][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-07 16:02:27.776][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:27.777][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:27.778][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:27.780][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-07 16:02:27.781][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-07 16:02:27.783][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:27.785][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:27.787][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-07 16:02:27.789][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:27.791][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-07 16:02:27.799][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-07 16:02:27.805][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2026-02-07 16:02:27.810][biodb::testThat]
biodb.INFO [2026-02-07 16:02:27.811][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-07 16:02:27.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:27.813][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:27.817][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2026-02-07 16:02:27.819][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:27.822][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-02-07 16:02:27.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:27.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:27.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:27.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:27.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:27.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:27.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:27.843][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:27.844][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:27.845][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.847][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:27.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:27.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.854][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:27.855][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:27.856][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.857][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.859][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:27.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:27.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.864][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:27.866][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:27.867][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.868][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:27.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:27.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.875][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:27.876][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:27.877][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.878][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:27.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:27.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.885][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:27.887][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:27.888][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.889][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:27.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:27.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.896][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:27.897][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:27.898][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.900][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.901][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:27.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:27.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.906][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-07 16:02:27.908][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:27.909][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.910][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.912][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-07 16:02:27.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:27.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.917][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:27.918][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:27.919][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.921][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:27.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:27.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.928][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:27.929][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:27.930][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.931][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:27.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:27.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.944][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:27.945][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:27.946][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.947][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:27.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:27.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.954][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:27.956][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:27.957][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.958][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.960][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:27.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:27.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.965][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-07 16:02:27.966][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:27.967][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.968][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-07 16:02:27.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:27.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.975][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:27.977][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:27.978][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.979][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.981][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:27.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:27.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.986][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:27.987][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:27.988][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.990][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.991][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:27.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:27.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:27.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:27.997][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-02-07 16:02:27.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:27.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.012][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-02-07 16:02:28.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.017][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.027][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-02-07 16:02:28.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.032][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.037][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.042][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-02-07 16:02:28.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.058][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-02-07 16:02:28.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:28.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:28.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.079][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.084][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.095][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:28.158][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2026-02-07 16:02:28.161][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:28.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:28.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.166][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:28.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:28.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.172][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:28.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:28.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.177][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:28.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:28.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:28.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:28.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.187][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:28.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:28.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.192][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:28.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:28.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.210][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.256][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.267][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:28.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.297][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.299][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.300][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.317][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-07 16:02:28.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.337][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-07 16:02:28.339][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.340][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.341][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.343][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-07 16:02:28.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-07 16:02:28.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.374][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-07 16:02:28.375][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.376][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.378][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-07 16:02:28.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.395][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:28.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:28.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:28.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:28.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.405][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:28.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:28.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.410][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:28.412][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:28.413][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.414][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:28.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:28.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.432][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:28.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:28.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.437][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:28.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:28.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.442][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:28.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:28.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.447][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:28.449][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:28.450][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.451][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.452][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:28.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:28.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.468][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.474][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.479][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.484][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.486][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.487][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.488][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.489][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.505][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.511][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.526][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.527][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.529][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.530][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.531][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.552][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.557][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.563][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.564][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.565][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.566][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.568][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.584][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.589][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.594][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.599][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.601][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.602][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.603][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.620][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.626][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.631][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.636][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.637][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.638][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.640][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.641][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.662][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.667][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.672][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.674][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.675][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.676][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.677][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.693][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.703][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.708][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.713][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.715][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.716][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.717][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:28.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:28.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:28.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:28.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.745][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:28.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:28.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.750][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:28.751][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:28.752][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.753][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:28.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:28.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.786][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.787][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.789][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.790][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:28.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:28.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:28.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:28.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:28.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:28.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.822][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:28.824][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:28.825][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.826][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:28.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:28.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.843][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:28.845][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:28.846][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.847][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.854][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.855][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:28.856][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.858][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.864][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.865][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:28.867][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.868][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.874][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.876][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:28.877][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.878][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.889][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.891][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:28.892][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.893][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.900][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.901][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:28.903][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.904][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.910][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:28.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:28.913][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.914][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.921][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:28.922][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:28.924][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.925][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.931][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.933][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:28.934][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.935][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.941][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:28.943][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:28.944][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.945][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.952][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.953][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:28.954][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.955][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.962][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.963][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:28.965][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.966][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.972][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:28.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:28.975][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.976][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.983][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.984][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:28.985][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.987][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:28.993][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.995][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:28.996][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:28.997][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.004][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2026-02-07 16:02:29.006][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:29.007][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-02-07 16:02:29.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:29.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:29.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:29.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:29.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:29.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:29.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:29.025][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.027][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.029][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.036][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.037][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.039][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.040][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.041][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.047][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.048][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.049][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.050][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.052][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.057][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.059][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.060][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.061][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.068][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.069][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.070][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.072][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.073][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.083][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.085][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.086][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.087][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.094][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-07 16:02:29.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.097][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.098][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.099][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-07 16:02:29.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.104][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:29.106][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:29.107][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.108][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.110][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:29.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:29.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.115][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:29.116][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:29.118][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.119][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:29.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:29.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.126][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.127][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.128][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.129][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.136][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:29.137][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:29.139][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.140][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.142][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:29.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:29.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.147][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-07 16:02:29.148][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.149][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.151][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-07 16:02:29.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.158][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.159][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.160][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.161][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.163][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.168][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.169][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.171][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.172][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.173][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.179][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-02-07 16:02:29.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.184][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.194][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-02-07 16:02:29.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.199][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.204][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.209][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-02-07 16:02:29.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.215][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.220][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.225][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-02-07 16:02:29.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.230][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.235][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.240][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-02-07 16:02:29.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:29.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:29.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.266][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.271][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.281][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:29.317][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2026-02-07 16:02:29.319][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:29.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:29.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.324][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:29.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:29.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.329][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:29.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:29.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.335][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:29.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:29.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.340][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:29.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:29.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.345][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:29.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:29.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.350][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:29.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:29.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.366][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.411][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.416][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.421][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:29.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.468][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.469][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.470][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.471][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:29.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:29.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.505][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.506][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.507][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:29.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.540][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.542][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.543][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.544][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:29.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:29.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:29.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.566][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:29.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:29.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.571][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:29.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:29.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.576][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:29.578][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:29.579][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.580][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.581][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:29.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:29.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.597][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:29.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:29.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.602][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:29.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:29.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.607][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:29.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:29.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.613][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:29.614][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:29.620][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.621][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.623][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:29.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:29.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.638][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.644][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.649][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.654][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.656][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.657][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.658][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.660][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:29.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.675][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.681][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.686][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.691][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.693][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.694][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.695][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.696][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:29.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.730][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.732][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.733][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.734][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:29.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:29.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:29.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:29.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:29.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:29.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:29.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.769][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:29.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:29.772][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.773][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:29.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:29.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.791][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.797][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.802][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.813][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.814][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.815][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.817][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.818][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:29.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.834][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.840][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.845][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.856][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.857][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.858][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.860][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.861][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:29.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.881][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.893][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.911][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.916][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.918][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.926][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.927][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.928][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:29.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.965][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.966][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.967][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.969][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.970][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:29.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.986][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:29.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:29.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:29.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:30.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.002][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:30.004][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:30.005][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.006][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:30.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:30.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.024][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:30.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:30.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:30.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:30.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.040][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:30.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:30.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.045][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:30.046][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:30.048][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.049][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:30.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:30.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.066][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:30.068][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:30.069][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.070][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.077][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:30.078][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-07 16:02:30.079][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.081][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.087][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:30.089][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-07 16:02:30.090][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.091][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.098][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:30.099][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-07 16:02:30.101][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.102][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.109][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:30.110][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:30.112][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.113][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.120][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:30.121][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:30.122][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.124][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.130][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:30.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:30.133][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.135][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.141][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:30.143][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:30.144][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.146][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.152][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:30.154][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:30.155][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.156][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.163][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-07 16:02:30.164][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-07 16:02:30.166][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.167][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.173][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:30.175][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:30.176][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.177][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.184][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:30.186][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:30.187][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.188][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.195][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:30.196][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:30.198][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.199][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.206][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:30.207][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-07 16:02:30.208][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.209][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.216][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:30.218][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-07 16:02:30.219][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.220][ef$get] fields variable is a list.
biodb.INFO [2026-02-07 16:02:30.230][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.232][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-07 16:02:30.237][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.239][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:30.242][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-07 16:02:30.246][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-07 16:02:30.248][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:30.249][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:30.250][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:30.252][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:30.253][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:30.254][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:30.312][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.314][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-07 16:02:30.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.316][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:30.320][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:30.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:30.323][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.324][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:30.326][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2026-02-07 16:02:30.338][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-07 16:02:30.409][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:30.411][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:30.413][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:30.414][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:30.415][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:30.417][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:30.418][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:30.475][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.477][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-07 16:02:30.478][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.479][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:30.489][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-07 16:02:30.490][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:30.492][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:30.494][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:30.495][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:30.496][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:30.498][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:30.499][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:30.563][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.564][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-07 16:02:30.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.567][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:30.572][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-07 16:02:30.574][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:30.575][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:30.577][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:30.578][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:30.579][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:30.580][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:30.582][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:30.639][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.640][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-07 16:02:30.642][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.643][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:30.701][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.703][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-07 16:02:30.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.705][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:30.770][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.771][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:30.773][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.774][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:30.832][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.834][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:30.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.836][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-02-07 16:02:30.908][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:30.909][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:30.911][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.912][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:30.913][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:30.914][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:30.916][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:30.917][ef$get] fields variable is a list.
biodb.INFO [2026-02-07 16:02:30.919][biodb::testThat]
biodb.INFO [2026-02-07 16:02:30.920][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2026-02-07 16:02:30.921][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:30.923][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:30.932][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-07 16:02:30.934][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:30.936][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:30.937][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:30.938][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:30.940][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:30.941][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:30.942][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:31.000][biodb::testThat]
biodb.INFO [2026-02-07 16:02:31.002][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2026-02-07 16:02:31.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:31.004][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:31.008][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-07 16:02:31.009][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-07 16:02:31.011][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:31.013][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:31.014][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:31.015][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:31.017][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:31.018][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:31.083][biodb::testThat]
biodb.INFO [2026-02-07 16:02:31.084][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2026-02-07 16:02:31.085][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:31.087][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:31.090][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-07 16:02:31.092][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-07 16:02:31.093][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:31.095][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:31.096][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:31.098][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:31.099][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:31.100][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:31.158][biodb::testThat]
biodb.INFO [2026-02-07 16:02:31.159][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2026-02-07 16:02:31.161][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:31.162][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:31.166][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-07 16:02:31.167][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-07 16:02:31.169][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:31.170][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:31.172][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:31.173][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:31.174][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:31.176][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-02-07 16:02:31.238][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:31.239][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:31.241][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:31.242][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:31.243][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:31.245][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:31.246][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:31.247][ef$get] fields variable is a list.
biodb.INFO [2026-02-07 16:02:31.249][biodb::testThat]
biodb.INFO [2026-02-07 16:02:31.250][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2026-02-07 16:02:31.251][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:31.253][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:31.256][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-07 16:02:31.258][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-07 16:02:31.259][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:31.261][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:31.262][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:31.263][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:31.265][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:31.266][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:31.324][biodb::testThat]
biodb.INFO [2026-02-07 16:02:31.325][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2026-02-07 16:02:31.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:31.328][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:31.331][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-07 16:02:31.333][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-07 16:02:31.335][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:31.336][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:31.337][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:31.339][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:31.340][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:31.341][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-07 16:02:31.404][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-07 16:02:31.405][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2026-02-07 16:02:31.406][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-07 16:02:31.408][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:31.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:31.410][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.412][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-07 16:02:31.418][biodb::testContext]
biodb.INFO [2026-02-07 16:02:31.420][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:31.421][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2026-02-07 16:02:31.422][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:31.423][biodb::testContext]
biodb.INFO [2026-02-07 16:02:31.426][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:31.428][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:31.432][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:31.434][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-07 16:02:31.435][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-07 16:02:31.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.440][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-07 16:02:31.441][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-07 16:02:31.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.446][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-07 16:02:31.447][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-07 16:02:31.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.452][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-07 16:02:31.453][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-07 16:02:31.454][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-07 16:02:31.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.459][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-07 16:02:31.460][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-07 16:02:31.462][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-07 16:02:31.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.467][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-07 16:02:31.468][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-07 16:02:31.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.473][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-07 16:02:31.474][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-07 16:02:31.475][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-07 16:02:31.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.480][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-07 16:02:31.481][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-07 16:02:31.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.486][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-07 16:02:31.487][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-07 16:02:31.488][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-07 16:02:31.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.493][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:31.494][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-07 16:02:31.496][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-07 16:02:31.497][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-07 16:02:31.498][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-07 16:02:31.500][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-07 16:02:31.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.504][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-07 16:02:31.506][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-07 16:02:31.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.510][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-07 16:02:31.512][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-07 16:02:31.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.521][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-07 16:02:31.523][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-07 16:02:31.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.528][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-07 16:02:31.529][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-07 16:02:31.530][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-07 16:02:31.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.535][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:31.536][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-07 16:02:31.547][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-07 16:02:31.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.552][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-07 16:02:31.553][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-07 16:02:31.554][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-07 16:02:31.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.559][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-07 16:02:31.561][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.562][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-07 16:02:31.564][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.565][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:31.566][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.567][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.569][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.570][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.571][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:31.572][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:31.574][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.575][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-07 16:02:31.576][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:31.578][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.580][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:31.580][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:31.580][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:31.580][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:31.580][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:31.581][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:31.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:31.584][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:31.585][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:31.586][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:31.587][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:31.588][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.590][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.591][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:31.592][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:31.593][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.595][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.596][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-07 16:02:31.598][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.600][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:31.601][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.602][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:31.603][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.605][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.606][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.607][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.609][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:31.610][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:31.611][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.612][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-07 16:02:31.614][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:31.615][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.616][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.618][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:31.618][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:31.618][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:31.618][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:31.618][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:31.619][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:31.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:31.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:31.622][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:31.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:31.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:31.626][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.627][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.629][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:31.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:31.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.632][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.634][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-07 16:02:31.636][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.637][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-07 16:02:31.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:31.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.643][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.644][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.645][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.646][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:31.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:31.649][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.650][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-07 16:02:31.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:31.653][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.654][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.655][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.657][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:31.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:31.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:31.660][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:31.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:31.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:31.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.665][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.667][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:31.668][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:31.669][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.670][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.672][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-07 16:02:31.674][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.676][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:31.677][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.678][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:31.679][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.681][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.682][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.683][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.685][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:31.686][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:31.687][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.689][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-07 16:02:31.690][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:31.691][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.693][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:31.698][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.700][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:31.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:31.703][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:31.704][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:31.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:31.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:31.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:31.709][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.710][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:31.711][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:31.713][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:31.714][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:31.716][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:31.717][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.811][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-07 16:02:31.812][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-07 16:02:31.814][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-07 16:02:31.816][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-07 16:02:31.818][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-07 16:02:31.820][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-07 16:02:31.821][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:31.823][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:31.825][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-07 16:02:31.827][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-07 16:02:31.829][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-07 16:02:31.831][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-07 16:02:31.832][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:31.834][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:31.836][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:31.838][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:31.839][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-07 16:02:31.841][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-07 16:02:31.843][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-07 16:02:31.845][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-07 16:02:31.846][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-07 16:02:31.848][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-07 16:02:31.850][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-07 16:02:31.852][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-07 16:02:31.854][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-07 16:02:31.856][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-07 16:02:31.858][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-07 16:02:31.859][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-07 16:02:31.869][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-07 16:02:31.871][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-07 16:02:31.873][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-07 16:02:31.875][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-07 16:02:31.877][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-07 16:02:31.878][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-07 16:02:31.880][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-07 16:02:31.882][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-07 16:02:31.884][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-07 16:02:31.885][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-07 16:02:31.887][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-07 16:02:31.889][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-07 16:02:31.891][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-07 16:02:31.892][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-07 16:02:31.894][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-07 16:02:31.896][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-07 16:02:31.898][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-07 16:02:31.899][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:31.901][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-07 16:02:31.903][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-07 16:02:31.905][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-07 16:02:31.906][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-07 16:02:31.908][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-07 16:02:31.910][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-07 16:02:31.912][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-07 16:02:31.913][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-07 16:02:31.915][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-07 16:02:31.917][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-07 16:02:31.919][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-07 16:02:31.920][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-07 16:02:31.922][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-07 16:02:31.924][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-07 16:02:31.926][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-07 16:02:31.927][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-07 16:02:31.929][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-07 16:02:31.931][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-07 16:02:31.933][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-07 16:02:31.934][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-07 16:02:31.936][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-07 16:02:31.938][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-07 16:02:31.939][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-07 16:02:31.941][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-07 16:02:31.943][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-07 16:02:31.945][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-07 16:02:31.946][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-07 16:02:31.948][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-07 16:02:31.950][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-07 16:02:31.952][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-07 16:02:31.953][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-07 16:02:31.955][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-07 16:02:31.957][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-07 16:02:31.959][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-07 16:02:31.961][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-07 16:02:31.962][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-07 16:02:31.964][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-07 16:02:31.966][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-07 16:02:31.968][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:31.969][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:31.970][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.973][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:31.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:31.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:31.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:31.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:31.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:31.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:31.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:31.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:31.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:31.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:31.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:32.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:32.110][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:32.112][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-07 16:02:32.115][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.116][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-07 16:02:32.117][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.118][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:32.120][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.121][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.122][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.123][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.125][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-07 16:02:32.126][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:32.127][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.128][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-07 16:02:32.130][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:32.131][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-07 16:02:32.131][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-07 16:02:32.132][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:32.134][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:32.135][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:32.136][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:32.137][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:32.138][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:32.140][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:32.141][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:32.142][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.143][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-07 16:02:32.143][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-07 16:02:32.144][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:32.145][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:32.147][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.148][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:32.150][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-07 16:02:32.152][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.153][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-07 16:02:32.154][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.156][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:32.157][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.158][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.159][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.161][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.162][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:32.163][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:32.164][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.166][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-07 16:02:32.167][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:32.168][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-07 16:02:32.168][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-07 16:02:32.168][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-07 16:02:32.168][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-07 16:02:32.168][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-07 16:02:32.168][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-07 16:02:32.170][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:32.171][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:32.172][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:32.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:32.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:32.176][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:32.177][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:32.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:32.179][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.180][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:32.180][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:32.182][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:32.183][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:32.184][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.185][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:32.187][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-07 16:02:32.189][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:32.191][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-07 16:02:32.192][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.193][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:32.195][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.196][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.197][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.199][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.200][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:32.201][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:32.202][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.204][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-07 16:02:32.210][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.211][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-07 16:02:32.213][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:32.215][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:32.215][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:32.215][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:32.216][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-07 16:02:32.218][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:32.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:32.221][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:32.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:32.223][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:32.224][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.225][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:32.225][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:32.225][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-07 16:02:32.227][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:32.228][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:32.229][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.230][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-07 16:02:32.232][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-07 16:02:32.234][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.235][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-07 16:02:32.237][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.238][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:32.239][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.240][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.242][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.243][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.244][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:32.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:32.247][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.248][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-07 16:02:32.249][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:32.250][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-07 16:02:32.250][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-07 16:02:32.252][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:32.253][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:32.254][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-07 16:02:32.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:32.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:32.258][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:32.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:32.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:32.261][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:32.262][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:32.262][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-07 16:02:32.262][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-07 16:02:32.264][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:32.265][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:32.266][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:32.267][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-07 16:02:32.269][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-07 16:02:32.271][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:32.273][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:32.274][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-07 16:02:32.276][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:32.278][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-07 16:02:32.284][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-07 16:02:32.289][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2026-02-07 16:02:32.294][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.295][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-07 16:02:32.297][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:32.298][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:32.301][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2026-02-07 16:02:32.303][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:32.306][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2026-02-07 16:02:32.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:32.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:32.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:32.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:32.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:32.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:32.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:32.323][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.326][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.327][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.334][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.335][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.336][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.337][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.344][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.349][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:32.403][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2026-02-07 16:02:32.405][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:32.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:32.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.410][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-07 16:02:32.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-07 16:02:32.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.415][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:32.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-07 16:02:32.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.421][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:32.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.426][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:32.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:32.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.431][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:32.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:32.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.437][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:32.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:32.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.453][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.496][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.501][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.506][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-07 16:02:32.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.535][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.536][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.538][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.539][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.560][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.565][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.576][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.577][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.578][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.579][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.581][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.596][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:32.597][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:32.599][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.600][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:32.606][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.608][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:32.609][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:32.610][ef$get] fields variable is a list.
biodb.INFO [2026-02-07 16:02:32.620][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.622][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-07 16:02:32.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:32.624][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:32.627][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-02-07 16:02:32.631][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:32.633][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:32.634][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:32.635][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:32.636][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:32.638][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:32.639][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-07 16:02:32.696][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.697][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-07 16:02:32.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:32.699][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.707][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.709][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-07 16:02:32.710][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:32.711][biodb::testThat]
biodb.WARN [2026-02-07 16:02:32.714][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-07 16:02:32.718][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-07 16:02:32.735][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.736][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-07 16:02:32.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:32.738][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:32.743][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-02-07 16:02:32.745][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-02-07 16:02:32.747][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-07 16:02:32.748][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-02-07 16:02:32.749][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:32.751][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-07 16:02:32.752][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-07 16:02:32.753][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-07 16:02:32.812][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.813][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-07 16:02:32.815][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:32.816][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-07 16:02:32.880][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.881][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-07 16:02:32.883][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:32.884][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-07 16:02:32.943][biodb::testThat]
biodb.INFO [2026-02-07 16:02:32.944][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:32.946][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:32.947][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-07 16:02:33.006][biodb::testThat]
biodb.INFO [2026-02-07 16:02:33.008][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:33.009][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:33.010][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-07 16:02:33.076][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-07 16:02:33.078][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2026-02-07 16:02:33.079][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-07 16:02:33.080][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:33.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:33.082][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:33.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:33.085][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:33.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$getEntryPageUrl(id)
 12.                     └─private$doGetEntryPageUrl(entry.id)
 13.                       └─base::vapply(id, fct, FUN.VALUE = "")
 14.                         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$getEntryPageUrl(id)
 14.                         └─private$doGetEntryPageUrl(entry.id)
 15.                           └─base::vapply(id, fct, FUN.VALUE = "")
 16.                             └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 15.                           └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 16.                             └─self$getEntryPageUrl(id)
 17.                               └─private$doGetEntryPageUrl(entry.id)
 18.                                 └─base::vapply(id, fct, FUN.VALUE = "")
 19.                                   └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)

[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
Error:
! Test failures.
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
  Error:
  ! Test failures.
  Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log’
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)