Long Tests report for BioC 3.22 - CHECK results for biodbNcbi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4893
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4687
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*

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: 2026-03-28 16:01:22 -0400 (Sat, 28 Mar 2026)

EndedAt: 2026-03-28 16:02:34 -0400 (Sat, 28 Mar 2026)

EllapsedTime: 71.9 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"
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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 [2026-03-28 16:02:21.104][biodb::testContext]
biodb.INFO [2026-03-28 16:02:21.108][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:21.109][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2026-03-28 16:02:21.110][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:21.112][biodb::testContext]
biodb.INFO [2026-03-28 16:02:21.118][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:21.120][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:21.128][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:21.129][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:02:21.131][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:02:21.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:21.135][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:02:21.160][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:02:21.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.163][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[2026-03-28 16:02:21.164][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:02:21.166][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:02:21.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:21.170][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:02:21.172][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:02:21.173][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:02:21.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.176][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[2026-03-28 16:02:21.178][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:02:21.179][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:02:21.180][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:02:21.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:21.185][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:02:21.186][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:02:21.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.190][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[2026-03-28 16:02:21.191][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:02:21.192][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:02:21.194][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:02:21.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:21.198][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:02:21.199][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:02:21.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.203][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[2026-03-28 16:02:21.204][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:02:21.205][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:02:21.207][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:02:21.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:21.211][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:21.213][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:02:21.214][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:02:21.215][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:02:21.217][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:02:21.218][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:02:21.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.221][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[2026-03-28 16:02:21.222][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:02:21.224][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:02:21.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:21.228][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:02:21.230][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:02:21.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.233][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[2026-03-28 16:02:21.234][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:02:21.236][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:02:21.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:21.240][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:02:21.241][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:02:21.243][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:02:21.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.246][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[2026-03-28 16:02:21.247][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:21.249][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:02:21.259][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:02:21.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:21.264][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:02:21.265][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:02:21.267][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:02:21.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.270][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[2026-03-28 16:02:21.274][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:02:21.318][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.346][self$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[2026-03-28 16:02:21.347][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.349][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:21.350][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.351][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.353][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.354][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.355][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:21.356][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:21.358][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.359][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:02:21.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:21.362][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.363][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.364][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:21.364][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:21.364][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:21.364][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:21.364][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:21.366][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:21.367][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.369][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:21.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.372][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.373][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.374][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.375][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:21.376][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:21.378][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.379][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.380][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:02:21.383][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.384][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:21.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.387][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:21.388][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.389][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.391][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.392][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.393][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:21.395][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:21.396][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.397][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:02:21.398][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:21.400][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.401][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.402][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:21.402][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:21.402][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:21.402][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:21.402][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:21.404][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:21.405][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.408][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:21.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.413][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.414][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:21.415][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:21.416][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.418][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.419][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:02:21.422][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.423][self$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[2026-03-28 16:02:21.424][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.425][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:21.427][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.428][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.429][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.431][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.432][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:21.433][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:21.434][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.436][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:02:21.437][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:21.438][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.439][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.441][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.442][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:21.443][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.446][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:21.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.449][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.450][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.452][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:21.453][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:21.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.455][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.457][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:02:21.459][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.460][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:21.462][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.463][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:21.464][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.467][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.468][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.469][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:21.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:21.472][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.473][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:02:21.474][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:21.476][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.477][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.478][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.479][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:21.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.483][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:21.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.487][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.488][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.489][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:21.490][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:21.491][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.493][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.497][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:21.498][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.499][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[2026-03-28 16:02:21.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.505][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[2026-03-28 16:02:21.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.511][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[2026-03-28 16:02:21.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.517][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[2026-03-28 16:02:21.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.523][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[2026-03-28 16:02:21.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.529][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[2026-03-28 16:02:21.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.535][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[2026-03-28 16:02:21.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.541][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[2026-03-28 16:02:21.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.547][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[2026-03-28 16:02:21.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.552][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[2026-03-28 16:02:21.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.558][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[2026-03-28 16:02:21.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.564][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[2026-03-28 16:02:21.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.570][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[2026-03-28 16:02:21.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.576][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[2026-03-28 16:02:21.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.582][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[2026-03-28 16:02:21.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.588][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[2026-03-28 16:02:21.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.594][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[2026-03-28 16:02:21.595][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:02:21.605][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:02:21.607][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:02:21.609][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:02:21.611][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:02:21.613][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:02:21.615][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:21.617][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:21.619][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:02:21.621][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:02:21.623][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:02:21.624][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:02:21.626][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:21.628][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:21.630][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:21.631][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:21.633][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:02:21.635][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:02:21.637][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:02:21.638][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:02:21.640][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:02:21.642][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:02:21.643][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:02:21.645][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:02:21.647][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:02:21.649][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:02:21.650][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:02:21.652][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:02:21.654][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:02:21.655][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:02:21.657][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:02:21.659][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:02:21.661][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:02:21.662][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:02:21.664][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:02:21.666][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:02:21.668][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:02:21.669][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:02:21.671][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:02:21.673][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:02:21.674][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:02:21.676][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:02:21.678][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:02:21.680][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:02:21.681][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:02:21.683][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:21.685][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:02:21.687][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:02:21.688][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:02:21.690][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:02:21.692][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:02:21.694][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:02:21.695][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:02:21.697][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:02:21.699][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:02:21.700][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:02:21.702][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:02:21.704][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:02:21.706][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:02:21.707][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:02:21.709][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:02:21.711][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:02:21.712][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:02:21.714][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:02:21.716][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:02:21.718][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:02:21.719][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:02:21.721][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:02:21.723][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:02:21.725][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:02:21.726][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:02:21.728][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:02:21.730][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:02:21.731][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:02:21.733][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:02:21.735][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:02:21.737][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:02:21.738][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:02:21.740][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:02:21.742][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:02:21.744][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:02:21.745][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:02:21.747][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:02:21.755][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:02:21.757][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:21.760][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:21.762][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.764][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.765][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.DEBUG[2026-03-28 16:02:21.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.778][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[2026-03-28 16:02:21.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.786][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[2026-03-28 16:02:21.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.794][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[2026-03-28 16:02:21.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.802][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[2026-03-28 16:02:21.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.810][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[2026-03-28 16:02:21.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.818][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[2026-03-28 16:02:21.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.825][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[2026-03-28 16:02:21.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.833][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[2026-03-28 16:02:21.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.841][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[2026-03-28 16:02:21.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.849][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[2026-03-28 16:02:21.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.861][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[2026-03-28 16:02:21.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.869][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[2026-03-28 16:02:21.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.877][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[2026-03-28 16:02:21.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.884][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[2026-03-28 16:02:21.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.892][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[2026-03-28 16:02:21.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:21.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:21.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:21.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:21.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:21.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:21.900][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[2026-03-28 16:02:21.902][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:21.915][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-03-28 16:02:21.918][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.919][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-03-28 16:02:21.920][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.922][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:21.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.924][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.925][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.927][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.928][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-03-28 16:02:21.929][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:21.930][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.932][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-03-28 16:02:21.933][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:21.934][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-03-28 16:02:21.934][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-03-28 16:02:21.935][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.937][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.938][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:21.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.940][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.941][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:21.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.945][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.946][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-28 16:02:21.946][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-03-28 16:02:21.947][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:21.948][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:21.950][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.951][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.952][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-03-28 16:02:21.955][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.956][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-03-28 16:02:21.957][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.958][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:21.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.962][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.963][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.965][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:21.966][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:21.967][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.968][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-03-28 16:02:21.970][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:21.971][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-03-28 16:02:21.971][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-03-28 16:02:21.971][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-03-28 16:02:21.971][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-03-28 16:02:21.971][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-03-28 16:02:21.971][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-03-28 16:02:21.972][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.974][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:21.975][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:21.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.978][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:21.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:21.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:21.982][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.983][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:21.983][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:21.984][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:21.985][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:21.987][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.988][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:21.989][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-28 16:02:21.992][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:21.993][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-03-28 16:02:21.994][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.995][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:21.997][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:21.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:21.999][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.000][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:22.002][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:22.003][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:22.004][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.005][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-03-28 16:02:22.007][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.008][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:22.010][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:22.011][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:22.011][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:22.011][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:22.012][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-28 16:02:22.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:22.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:22.016][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:22.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:22.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:22.019][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:22.020][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:22.020][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:22.020][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-28 16:02:22.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:22.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:22.024][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.025][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-28 16:02:22.027][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-28 16:02:22.029][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.031][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-03-28 16:02:22.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:22.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:22.037][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.038][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:22.039][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:22.040][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:22.042][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.043][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-03-28 16:02:22.044][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:22.045][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-03-28 16:02:22.045][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-28 16:02:22.047][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:22.048][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:22.049][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-28 16:02:22.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:22.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:22.053][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:22.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:22.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:22.056][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:22.057][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:22.057][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:22.057][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-28 16:02:22.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:22.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:22.061][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:22.062][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-28 16:02:22.070][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-03-28 16:02:22.072][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:22.074][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:22.076][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-03-28 16:02:22.078][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:22.079][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-03-28 16:02:22.101][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-03-28 16:02:22.118][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2026-03-28 16:02:22.133][biodb::testThat]
biodb.INFO [2026-03-28 16:02:22.135][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-28 16:02:22.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:22.137][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:22.141][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2026-03-28 16:02:22.143][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:22.147][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-03-28 16:02:22.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:22.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:22.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:22.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:22.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:22.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:22.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:22.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.216][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:22.233][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.234][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.235][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.272][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:22.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.277][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.282][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.293][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:22.383][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2026-03-28 16:02:22.386][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.391][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.428][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:22.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:22.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.433][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:22.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:22.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.438][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:22.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:22.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.443][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:22.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:22.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.471][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.516][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.555][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.557][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.558][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.559][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.576][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:22.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.581][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.591][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.596][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:22.597][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.598][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.599][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.601][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:22.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.616][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.617][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.618][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.620][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.626][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.627][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.628][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.630][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.652][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2026-03-28 16:02:22.700][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:22.701][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-03-28 16:02:22.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:22.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:22.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:22.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:22.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:22.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:22.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:22.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.759][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:22.760][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.761][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.763][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.765][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:22.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.770][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.775][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.785][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:22.855][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2026-03-28 16:02:22.883][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.889][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:22.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.894][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:22.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:22.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:22.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:22.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:22.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:22.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.909][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:22.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:22.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.926][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:22.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:22.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.970][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.975][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:22.980][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:22.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:22.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:23.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:23.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:23.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:23.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:23.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:23.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.024][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:23.025][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:23.026][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.028][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:23.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:23.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.045][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:23.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.055][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.060][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.065][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:23.067][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.068][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.069][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.070][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-03-28 16:02:23.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.086][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.088][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:23.089][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.090][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:23.097][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:23.099][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:23.100][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:23.101][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:02:23.112][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.113][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-28 16:02:23.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:23.116][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:23.119][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2026-03-28 16:02:23.124][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2026-03-28 16:02:23.128][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-03-28 16:02:23.130][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:23.131][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-28 16:02:23.133][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:23.134][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-03-28 16:02:23.326][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.328][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-28 16:02:23.329][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:23.331][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.340][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.342][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-28 16:02:23.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:23.344][biodb::testThat]
biodb.WARN [2026-03-28 16:02:23.367][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-03-28 16:02:23.393][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-03-28 16:02:23.404][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.406][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-28 16:02:23.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:23.409][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:23.433][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2026-03-28 16:02:23.505][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:23.549][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-03-28 16:02:23.550][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:23.551][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-28 16:02:23.553][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:23.554][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-03-28 16:02:23.644][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.646][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-28 16:02:23.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:23.648][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-03-28 16:02:23.710][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.712][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-28 16:02:23.713][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:23.714][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.724][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.726][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:23.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:23.728][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-03-28 16:02:23.787][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.789][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:23.790][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:23.791][biodb::testThat]
biodb.INFO [2026-03-28 16:02:23.799][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:02:23.801][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-03-28 16:02:23.802][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:02:23.803][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:23.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:23.805][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:23.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:23.808][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-28 16:02:23.822][biodb::testContext]
biodb.INFO [2026-03-28 16:02:23.824][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:23.825][biodb::testContext] Test context - Gene long tests
biodb.INFO [2026-03-28 16:02:23.826][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:23.827][biodb::testContext]
biodb.INFO [2026-03-28 16:02:23.830][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:23.832][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:23.836][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:23.837][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:02:23.839][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:02:23.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.842][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[2026-03-28 16:02:23.843][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:02:23.873][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:02:23.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:23.877][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:02:23.879][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:02:23.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.882][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[2026-03-28 16:02:23.883][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:02:23.885][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:02:23.886][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:02:23.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:23.891][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:02:23.892][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:02:23.893][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:02:23.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.897][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[2026-03-28 16:02:23.898][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:02:23.899][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:02:23.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:23.904][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:02:23.905][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:02:23.906][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:02:23.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.910][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[2026-03-28 16:02:23.911][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:02:23.912][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:02:23.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:23.917][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:02:23.918][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:02:23.920][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:02:23.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.923][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[2026-03-28 16:02:23.924][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:23.925][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:02:23.927][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:02:23.928][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:02:23.929][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:02:23.931][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:02:23.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:23.935][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:02:23.937][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:02:23.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.940][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[2026-03-28 16:02:23.941][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:02:23.943][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:02:23.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:23.947][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:02:23.949][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:02:23.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.952][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[2026-03-28 16:02:23.953][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:02:23.955][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:02:23.956][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:02:23.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:23.961][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:23.962][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:02:23.973][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:02:23.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.977][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[2026-03-28 16:02:23.978][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:02:23.979][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:02:23.981][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:02:23.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:23.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:23.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:23.985][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:02:23.988][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:23.989][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-28 16:02:23.990][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:23.992][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:23.993][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:23.994][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:23.995][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:23.997][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:23.998][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:23.999][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:24.001][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.002][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:02:24.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:24.005][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.006][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.007][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:24.007][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:24.007][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:24.007][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:24.007][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:24.009][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:24.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:24.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.016][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.017][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.018][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:24.020][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:24.021][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.022][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.024][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:02:24.026][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.027][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:24.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:24.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.034][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.035][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.036][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:24.037][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:24.039][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.040][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:02:24.041][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:24.043][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.044][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.045][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:24.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:24.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:24.045][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:24.045][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:24.047][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:24.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.050][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:24.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.058][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.059][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.060][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:24.061][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:24.063][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.064][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.065][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:02:24.067][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.069][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-28 16:02:24.070][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.071][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:24.073][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.074][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.075][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.076][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.078][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:24.079][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:24.080][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.081][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:02:24.083][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:24.084][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.085][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.087][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.088][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:24.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.091][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:24.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.095][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.096][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.098][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:24.099][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:24.100][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.101][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.103][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:02:24.105][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.106][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:24.107][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:24.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.111][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.112][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.115][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:24.116][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:24.118][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.119][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:02:24.120][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:24.121][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.123][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.124][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.125][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:24.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.129][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:24.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.132][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.134][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.135][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:24.136][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:24.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.139][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.140][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:24.141][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.142][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[2026-03-28 16:02:24.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.148][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[2026-03-28 16:02:24.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.154][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[2026-03-28 16:02:24.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.159][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[2026-03-28 16:02:24.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.165][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[2026-03-28 16:02:24.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.171][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[2026-03-28 16:02:24.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.176][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[2026-03-28 16:02:24.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.182][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[2026-03-28 16:02:24.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.188][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[2026-03-28 16:02:24.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.193][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[2026-03-28 16:02:24.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.199][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[2026-03-28 16:02:24.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.205][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[2026-03-28 16:02:24.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.210][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[2026-03-28 16:02:24.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.216][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[2026-03-28 16:02:24.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.222][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[2026-03-28 16:02:24.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.227][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[2026-03-28 16:02:24.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.233][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[2026-03-28 16:02:24.234][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:02:24.236][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:02:24.238][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:02:24.240][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:02:24.241][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:02:24.243][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:02:24.245][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:24.247][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:24.252][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:02:24.254][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:02:24.256][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:02:24.257][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:02:24.259][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:24.261][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:24.263][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:24.264][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:24.266][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:02:24.268][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:02:24.269][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:02:24.271][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:02:24.273][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:02:24.275][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:02:24.276][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:02:24.278][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:02:24.280][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:02:24.282][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:02:24.283][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:02:24.285][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:02:24.287][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:02:24.289][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:02:24.290][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:02:24.292][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:02:24.294][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:02:24.296][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:02:24.297][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:02:24.299][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:02:24.301][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:02:24.303][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:02:24.304][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:02:24.306][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:02:24.308][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:02:24.310][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:02:24.312][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:02:24.313][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:02:24.315][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:02:24.317][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:24.319][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:02:24.320][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:02:24.322][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:02:24.324][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:02:24.326][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:02:24.327][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:02:24.329][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:02:24.331][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:02:24.333][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:02:24.334][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:02:24.336][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:02:24.338][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:02:24.340][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:02:24.341][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:02:24.343][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:02:24.345][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:02:24.347][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:02:24.348][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:02:24.350][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:02:24.352][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:02:24.354][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:02:24.355][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:02:24.357][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:02:24.359][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:02:24.361][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:02:24.362][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:02:24.364][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:02:24.366][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:02:24.368][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:02:24.370][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:02:24.371][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:02:24.373][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:02:24.375][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:02:24.377][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:02:24.379][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:02:24.381][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:02:24.382][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:02:24.384][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:02:24.386][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:24.387][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:24.389][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.391][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.392][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[2026-03-28 16:02:24.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.400][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[2026-03-28 16:02:24.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.408][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[2026-03-28 16:02:24.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.416][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[2026-03-28 16:02:24.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.424][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[2026-03-28 16:02:24.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.432][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[2026-03-28 16:02:24.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.440][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[2026-03-28 16:02:24.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.453][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[2026-03-28 16:02:24.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.461][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[2026-03-28 16:02:24.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.469][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[2026-03-28 16:02:24.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.477][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[2026-03-28 16:02:24.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.485][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[2026-03-28 16:02:24.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.493][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[2026-03-28 16:02:24.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.501][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[2026-03-28 16:02:24.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.509][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[2026-03-28 16:02:24.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.517][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[2026-03-28 16:02:24.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:24.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.525][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[2026-03-28 16:02:24.527][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:24.530][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-03-28 16:02:24.532][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.533][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-03-28 16:02:24.534][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.536][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:24.537][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.538][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.539][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.541][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.542][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-03-28 16:02:24.543][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:24.545][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.546][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-03-28 16:02:24.547][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:24.549][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-03-28 16:02:24.549][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-03-28 16:02:24.550][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.551][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.552][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:24.554][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.555][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.556][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:24.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.560][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.561][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-28 16:02:24.561][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-03-28 16:02:24.562][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:24.563][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:24.565][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.566][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.567][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-03-28 16:02:24.570][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.571][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-03-28 16:02:24.572][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.574][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:24.575][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.576][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.577][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.579][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.580][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:24.581][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:24.583][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.584][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-03-28 16:02:24.585][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:24.586][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-03-28 16:02:24.586][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-03-28 16:02:24.586][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-03-28 16:02:24.586][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-03-28 16:02:24.586][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-03-28 16:02:24.586][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-03-28 16:02:24.588][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.589][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:24.591][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:24.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:24.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.598][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.599][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:24.599][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:24.600][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:24.601][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:24.603][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.604][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.606][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-28 16:02:24.608][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.609][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-03-28 16:02:24.611][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.612][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:24.613][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.615][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.616][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.617][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.618][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:24.620][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:24.621][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.622][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-03-28 16:02:24.624][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$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[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.625][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:24.627][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.628][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:24.628][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:24.628][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:24.629][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-28 16:02:24.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.633][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:24.634][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.637][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.638][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:24.638][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:24.638][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-28 16:02:24.639][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:24.640][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:24.641][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.647][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-28 16:02:24.649][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-28 16:02:24.652][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.653][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-03-28 16:02:24.654][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.655][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:24.657][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.658][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.659][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.660][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.662][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:24.663][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:24.664][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.666][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-03-28 16:02:24.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-03-28 16:02:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-28 16:02:24.670][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:24.671][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:24.672][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-28 16:02:24.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.676][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:24.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:24.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:24.680][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:24.682][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:24.682][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:24.682][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-28 16:02:24.683][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:24.684][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:24.686][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:24.687][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-28 16:02:24.689][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-03-28 16:02:24.691][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:24.693][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:24.696][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-03-28 16:02:24.698][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:24.700][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-03-28 16:02:24.709][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2026-03-28 16:02:24.749][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2026-03-28 16:02:24.755][biodb::testThat]
biodb.INFO [2026-03-28 16:02:24.756][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-28 16:02:24.757][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:24.758][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:24.764][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2026-03-28 16:02:24.766][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:24.769][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2026-03-28 16:02:24.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:24.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:24.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:24.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:24.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:24.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:24.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:24.797][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.799][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.800][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.801][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.809][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:24.811][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:24.812][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.814][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.817][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:24.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:24.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.825][ef$get] Asked field names are: location.
biodb.TRACE[2026-03-28 16:02:24.827][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-03-28 16:02:24.828][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.829][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.831][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2026-03-28 16:02:24.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-03-28 16:02:24.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.836][ef$get] Asked field names are: symbol.
biodb.TRACE[2026-03-28 16:02:24.838][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-03-28 16:02:24.839][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.840][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.842][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2026-03-28 16:02:24.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-03-28 16:02:24.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.848][ef$get] Asked field names are: synonyms.
biodb.TRACE[2026-03-28 16:02:24.849][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:24.851][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.852][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.854][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2026-03-28 16:02:24.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:24.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.860][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-03-28 16:02:24.861][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-03-28 16:02:24.862][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.863][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.866][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-03-28 16:02:24.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-03-28 16:02:24.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.883][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:24.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:24.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.889][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-03-28 16:02:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-03-28 16:02:24.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.894][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-03-28 16:02:24.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-03-28 16:02:24.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.904][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-03-28 16:02:24.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-03-28 16:02:24.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:24.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:24.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:24.941][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2026-03-28 16:02:24.944][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:24.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:24.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.949][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:24.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:24.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.954][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:24.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:24.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.959][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:24.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:24.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:24.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:24.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:24.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:24.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:24.970][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2026-03-28 16:02:25.011][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-03-28 16:02:25.032][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2026-03-28 16:02:25.033][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2026-03-28 16:02:25.039][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:25.041][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-03-28 16:02:25.043][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:25.044][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-28 16:02:25.046][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:25.047][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-28 16:02:25.113][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.114][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-28 16:02:25.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:25.117][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:25.120][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2026-03-28 16:02:25.121][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2026-03-28 16:02:25.124][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-03-28 16:02:25.125][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:25.127][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:25.128][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:25.129][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:25.131][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-28 16:02:25.193][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.194][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-28 16:02:25.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:25.197][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:25.201][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:25.203][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:25.204][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:25.205][ef$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:25.207][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2026-03-28 16:02:25.219][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-03-28 16:02:25.220][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:25.222][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-03-28 16:02:25.224][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:25.225][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:25.226][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:25.228][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:25.261][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-28 16:02:25.344][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.345][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-28 16:02:25.347][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:25.348][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:25.358][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-03-28 16:02:25.359][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:25.361][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-03-28 16:02:25.362][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:25.364][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:25.365][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:25.366][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:25.367][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-28 16:02:25.431][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.432][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-28 16:02:25.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:25.435][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:25.440][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-03-28 16:02:25.441][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:25.443][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-03-28 16:02:25.445][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:25.446][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:25.447][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:25.449][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:25.450][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-28 16:02:25.511][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.512][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-28 16:02:25.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:25.515][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-28 16:02:25.574][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.576][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-28 16:02:25.577][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:25.578][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.588][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.589][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:25.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:25.592][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-03-28 16:02:25.654][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.656][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:25.657][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:25.658][biodb::testThat]
biodb.INFO [2026-03-28 16:02:25.666][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:02:25.668][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2026-03-28 16:02:25.669][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-03-28 16:02:25.670][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:02:25.671][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:25.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:25.673][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:25.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:25.676][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-28 16:02:25.682][biodb::testContext]
biodb.INFO [2026-03-28 16:02:25.683][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:25.684][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2026-03-28 16:02:25.685][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:25.687][biodb::testContext]
biodb.INFO [2026-03-28 16:02:25.689][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:25.691][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:25.696][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:25.697][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:02:25.698][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:02:25.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.702][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[2026-03-28 16:02:25.703][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:02:25.704][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:02:25.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:25.709][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:02:25.710][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:02:25.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.714][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[2026-03-28 16:02:25.715][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:02:25.716][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:02:25.718][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:02:25.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:25.722][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:02:25.723][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:02:25.725][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:02:25.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.728][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[2026-03-28 16:02:25.729][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:02:25.731][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:02:25.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:25.735][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:02:25.737][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:02:25.738][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:02:25.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.741][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[2026-03-28 16:02:25.743][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:02:25.744][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:02:25.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:25.749][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:02:25.750][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:02:25.751][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:02:25.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.755][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[2026-03-28 16:02:25.756][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:25.757][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:02:25.758][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:02:25.760][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:02:25.761][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:02:25.762][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:02:25.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:25.767][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:02:25.768][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:02:25.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.772][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[2026-03-28 16:02:25.773][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:02:25.774][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:02:25.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:25.779][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:02:25.780][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:02:25.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.788][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[2026-03-28 16:02:25.789][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:02:25.791][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:02:25.792][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:02:25.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:25.797][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:25.798][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:02:25.808][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:02:25.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.812][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[2026-03-28 16:02:25.813][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:02:25.814][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:02:25.815][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:02:25.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:25.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:25.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:25.821][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:02:25.823][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:25.824][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-28 16:02:25.825][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.827][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:25.828][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.829][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.831][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:25.832][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.833][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:25.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:25.836][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.837][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:02:25.838][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:25.840][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.841][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.842][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:25.842][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:25.842][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:25.842][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:25.842][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:25.844][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:25.845][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:25.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:25.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:25.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:25.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:25.855][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.857][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.861][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:25.863][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:25.866][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:25.869][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.872][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:02:25.877][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:25.879][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:25.881][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.884][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:25.887][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.890][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.892][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:25.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.897][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:25.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:25.902][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.904][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:02:25.907][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:25.909][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.912][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.914][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:25.914][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:25.914][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:25.914][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:25.914][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:25.917][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:25.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:25.921][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:25.924][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:25.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:25.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:25.931][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.933][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:25.937][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:25.940][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:25.942][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.945][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:02:25.948][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.951][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-28 16:02:25.953][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:25.958][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.960][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.962][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:25.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.967][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:25.970][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:25.972][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:25.975][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:02:25.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:25.979][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.981][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:25.983][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.985][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:25.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:25.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:25.991][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:25.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:25.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:25.996][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:25.997][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:25.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:26.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:26.001][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.003][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.004][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:02:26.007][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.008][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:26.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:26.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.017][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.021][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.022][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:26.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:26.025][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.027][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:02:26.028][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:26.029][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.031][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.032][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.033][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:26.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.037][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:26.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.041][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.042][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:26.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:26.046][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.047][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.049][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:26.050][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.051][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[2026-03-28 16:02:26.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.061][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[2026-03-28 16:02:26.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.067][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[2026-03-28 16:02:26.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.072][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[2026-03-28 16:02:26.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.078][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[2026-03-28 16:02:26.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.084][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[2026-03-28 16:02:26.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.090][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[2026-03-28 16:02:26.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.095][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[2026-03-28 16:02:26.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.101][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[2026-03-28 16:02:26.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.107][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[2026-03-28 16:02:26.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.113][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[2026-03-28 16:02:26.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.118][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[2026-03-28 16:02:26.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.124][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[2026-03-28 16:02:26.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.130][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[2026-03-28 16:02:26.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.137][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[2026-03-28 16:02:26.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.142][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[2026-03-28 16:02:26.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.148][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[2026-03-28 16:02:26.149][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:02:26.151][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:02:26.153][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:02:26.155][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:02:26.157][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:02:26.158][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:02:26.160][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:26.162][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:26.164][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:02:26.165][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:02:26.167][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:02:26.169][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:02:26.171][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:26.172][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:26.174][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:26.176][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:26.178][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:02:26.180][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:02:26.181][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:02:26.183][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:02:26.185][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:02:26.187][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:02:26.189][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:02:26.190][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:02:26.192][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:02:26.194][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:02:26.196][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:02:26.198][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:02:26.200][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:02:26.201][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:02:26.203][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:02:26.205][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:02:26.207][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:02:26.209][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:02:26.211][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:02:26.213][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:02:26.215][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:02:26.217][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:02:26.219][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:02:26.221][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:02:26.222][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:02:26.224][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:02:26.226][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:02:26.228][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:02:26.230][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:02:26.232][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:26.234][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:02:26.235][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:02:26.237][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:02:26.239][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:02:26.245][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:02:26.247][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:02:26.248][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:02:26.250][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:02:26.252][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:02:26.253][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:02:26.255][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:02:26.257][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:02:26.259][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:02:26.261][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:02:26.262][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:02:26.264][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:02:26.266][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:02:26.268][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:02:26.269][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:02:26.271][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:02:26.273][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:02:26.275][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:02:26.276][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:02:26.278][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:02:26.280][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:02:26.282][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:02:26.283][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:02:26.285][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:02:26.287][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:02:26.288][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:02:26.290][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:02:26.292][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:02:26.294][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:02:26.296][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:02:26.298][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:02:26.299][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:02:26.301][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:02:26.303][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:02:26.305][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:26.306][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:26.307][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.309][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.311][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[2026-03-28 16:02:26.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.318][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[2026-03-28 16:02:26.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.326][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[2026-03-28 16:02:26.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.334][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[2026-03-28 16:02:26.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.342][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[2026-03-28 16:02:26.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.350][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[2026-03-28 16:02:26.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.357][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[2026-03-28 16:02:26.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.365][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[2026-03-28 16:02:26.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.373][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[2026-03-28 16:02:26.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.381][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[2026-03-28 16:02:26.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.389][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[2026-03-28 16:02:26.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.397][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[2026-03-28 16:02:26.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.405][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[2026-03-28 16:02:26.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.413][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[2026-03-28 16:02:26.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.425][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[2026-03-28 16:02:26.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.433][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[2026-03-28 16:02:26.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:26.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.440][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[2026-03-28 16:02:26.443][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:26.445][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-03-28 16:02:26.447][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.449][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-03-28 16:02:26.450][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.451][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:26.452][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.454][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.455][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.456][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.457][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-03-28 16:02:26.459][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:26.460][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.461][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-03-28 16:02:26.462][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:26.464][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-03-28 16:02:26.464][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-03-28 16:02:26.465][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.466][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.467][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:26.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.471][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:26.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.475][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.476][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-28 16:02:26.476][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-03-28 16:02:26.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:26.478][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:26.479][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.481][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.482][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-03-28 16:02:26.485][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.486][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-03-28 16:02:26.487][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.488][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:26.490][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.491][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.492][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.493][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.494][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:26.496][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:26.497][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.498][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-03-28 16:02:26.499][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:26.501][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-03-28 16:02:26.501][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-03-28 16:02:26.501][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-03-28 16:02:26.501][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-03-28 16:02:26.501][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-03-28 16:02:26.501][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-03-28 16:02:26.502][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.503][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:26.505][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:26.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.508][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:26.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.512][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.513][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:26.513][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:26.514][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:26.515][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:26.517][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.518][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.519][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-28 16:02:26.522][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.523][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-03-28 16:02:26.524][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:26.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.529][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.531][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.532][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:26.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:26.534][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.536][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-03-28 16:02:26.537][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$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[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:26.540][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.541][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:26.541][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:26.541][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:26.543][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-28 16:02:26.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.546][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:26.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.550][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.551][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:26.551][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:26.551][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-28 16:02:26.552][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:26.554][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:26.555][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.556][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-28 16:02:26.558][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-28 16:02:26.560][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.561][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-03-28 16:02:26.563][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.564][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:26.565][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.566][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.568][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.569][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.570][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:26.572][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:26.574][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.576][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-03-28 16:02:26.577][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:26.579][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-03-28 16:02:26.579][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-28 16:02:26.581][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:26.582][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:26.584][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-28 16:02:26.586][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.588][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.590][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:26.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:26.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:26.610][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:26.616][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:26.616][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:26.616][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-28 16:02:26.620][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:26.623][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:26.629][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:26.692][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-28 16:02:26.697][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-03-28 16:02:26.700][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:26.703][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:26.714][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-03-28 16:02:26.717][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:26.721][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-03-28 16:02:26.736][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-28 16:02:26.745][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2026-03-28 16:02:26.754][biodb::testThat]
biodb.INFO [2026-03-28 16:02:26.756][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-28 16:02:26.758][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:26.760][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:26.766][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2026-03-28 16:02:26.769][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:26.776][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-03-28 16:02:26.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:26.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:26.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:26.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:26.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:26.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:26.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:26.811][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:26.813][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:26.816][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.818][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:26.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:26.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.829][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:26.832][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:26.834][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.836][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.839][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:26.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:26.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.848][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:26.851][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:26.853][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.856][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.859][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:26.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:26.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.868][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:26.871][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:26.873][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.875][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.878][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:26.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:26.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.887][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:26.890][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:26.892][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.894][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.897][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:26.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:26.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.907][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:26.910][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:26.912][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.915][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.917][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:26.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:26.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.928][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-28 16:02:26.930][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:26.933][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.935][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.938][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-28 16:02:26.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:26.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.948][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:26.951][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:26.953][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.956][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:26.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:26.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.968][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:26.971][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:26.973][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.975][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:26.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:26.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.988][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:26.990][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:26.992][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.993][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:26.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:26.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:26.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:26.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.001][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:27.002][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:27.004][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.005][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.007][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:27.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:27.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.015][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-28 16:02:27.017][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.019][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.021][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-28 16:02:27.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.028][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.030][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.031][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.032][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.040][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.045][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.046][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.048][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.049][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.050][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.056][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-03-28 16:02:27.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.061][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.071][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-03-28 16:02:27.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.087][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-03-28 16:02:27.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.097][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.102][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-03-28 16:02:27.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.108][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.113][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.118][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-03-28 16:02:27.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.124][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.129][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.134][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:27.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:27.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.139][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.144][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.155][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:27.193][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2026-03-28 16:02:27.196][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:27.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:27.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.201][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:27.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:27.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:27.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:27.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.212][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:27.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:27.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.218][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:27.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:27.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.249][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:27.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:27.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.255][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:27.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:27.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.273][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.318][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.323][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.328][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:27.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.358][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.359][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.360][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.361][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.381][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-28 16:02:27.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:27.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:27.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:27.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:27.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.399][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-28 16:02:27.400][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:27.401][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.403][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.404][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-28 16:02:27.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:27.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-28 16:02:27.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.437][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-28 16:02:27.444][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.445][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.446][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-28 16:02:27.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:27.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.465][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:27.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:27.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:27.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:27.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:27.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:27.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.480][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:27.482][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:27.483][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.484][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:27.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:27.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.502][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:27.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:27.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.507][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:27.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:27.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.512][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:27.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:27.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.517][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:27.519][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:27.520][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.521][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.522][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:27.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:27.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.539][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.544][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.549][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.554][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.556][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.557][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.558][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.560][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:27.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.575][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.581][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.586][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.591][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.592][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.594][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.595][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:27.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.617][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.622][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.628][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.629][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.635][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.636][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.638][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.654][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.659][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.664][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.670][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.671][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.672][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.673][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.697][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.702][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.707][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.709][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.710][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.711][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.734][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.739][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.744][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.746][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.747][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.748][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.749][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.766][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.771][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.776][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.782][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.783][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.784][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.785][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:27.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:27.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:27.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:27.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:27.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:27.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.819][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:27.820][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:27.827][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.828][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:27.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:27.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.861][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.863][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.864][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.865][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.866][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:27.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:27.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:27.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:27.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:27.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:27.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:27.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.898][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:27.899][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:27.900][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.901][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:27.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:27.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.918][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:27.920][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:27.921][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.923][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.929][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.931][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:27.932][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.933][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.940][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.941][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:27.942][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.944][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.950][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.952][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:27.953][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.954][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.961][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.963][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:27.964][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.965][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.972][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.974][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:27.975][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.976][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.983][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:27.984][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:27.985][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.987][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:27.993][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:27.995][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:27.996][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:27.997][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.004][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.006][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.007][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.008][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.015][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:28.016][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:28.018][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.025][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.032][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.034][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.035][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.036][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.043][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.044][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.045][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.047][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.053][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:28.055][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:28.056][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.057][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.064][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.065][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.067][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.068][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.075][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.076][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.078][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.079][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.103][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2026-03-28 16:02:28.104][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:28.106][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-03-28 16:02:28.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:28.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:28.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:28.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:28.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:28.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:28.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:28.124][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.126][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.127][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.128][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.135][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.136][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.138][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.139][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.141][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.147][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.148][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.149][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.151][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.152][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.158][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.160][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.161][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.162][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.170][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.171][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.173][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.174][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.176][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.181][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.183][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.184][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.186][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.193][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-28 16:02:28.195][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.196][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.198][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.199][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-03-28 16:02:28.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.205][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:28.206][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:28.207][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.209][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.210][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:28.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:28.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.215][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:28.221][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:28.223][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.224][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:28.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:28.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.232][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.233][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.234][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.235][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.242][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:28.244][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:28.245][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.246][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.248][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:28.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:28.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.253][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-28 16:02:28.254][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.255][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.257][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-03-28 16:02:28.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.263][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.265][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.266][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.267][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.269][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.274][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.275][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.277][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.278][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.285][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-03-28 16:02:28.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.290][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.295][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.300][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-03-28 16:02:28.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.305][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.310][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.315][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-03-28 16:02:28.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.320][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:28.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.330][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-03-28 16:02:28.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.335][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.345][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-03-28 16:02:28.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.350][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.355][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:28.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:28.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.365][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.370][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.381][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:28.422][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2026-03-28 16:02:28.424][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:28.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:28.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.429][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:28.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:28.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.434][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:28.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:28.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.440][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:28.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:28.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.445][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:28.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:28.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.450][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:28.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:28.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:28.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:28.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.473][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.516][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:28.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.554][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.555][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.556][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.557][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:28.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:28.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.598][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.599][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:28.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.632][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.633][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.634][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.635][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:28.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.653][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:28.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:28.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.658][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:28.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:28.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.663][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:28.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:28.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.668][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:28.669][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:28.671][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.672][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:28.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:28.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.689][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:28.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:28.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.694][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:28.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:28.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.699][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:28.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:28.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.704][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:28.705][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:28.707][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.708][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.709][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:28.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:28.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.725][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.735][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.740][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.742][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.743][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.744][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.745][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:28.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.761][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.766][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.776][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.782][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.783][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.784][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.785][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.787][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:28.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.817][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.819][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.820][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.821][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:28.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:28.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:28.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:28.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:28.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:28.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:28.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.853][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:28.855][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:28.856][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.857][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:28.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:28.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.890][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.891][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.892][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.894][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.895][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:28.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.911][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.916][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.926][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.928][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.929][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.930][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:28.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.947][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.952][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.962][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.968][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.969][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.970][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.971][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.973][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:28.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.988][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.994][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:28.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:28.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:28.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:29.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:29.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.004][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:29.006][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:29.007][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.008][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.010][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:29.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:29.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.025][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.036][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.041][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.042][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.043][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.045][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.046][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:29.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:29.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:29.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:29.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.072][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:29.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:29.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.077][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:29.079][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:29.080][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.081][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:29.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:29.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.098][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:29.099][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:29.101][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.102][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.108][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:29.110][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-03-28 16:02:29.111][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.112][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.119][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:29.120][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-03-28 16:02:29.121][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.123][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.129][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:29.131][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-03-28 16:02:29.132][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.133][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.140][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:29.141][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:29.142][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.144][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.156][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.158][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:29.159][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.161][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.168][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:29.169][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:29.170][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.172][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.178][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:29.179][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:29.181][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.182][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.188][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:29.190][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:29.191][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.192][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.199][ef$get] Asked field names are: logp.
biodb.TRACE[2026-03-28 16:02:29.200][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-03-28 16:02:29.201][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.203][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.209][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:29.210][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:29.212][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.213][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.219][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:29.221][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:29.222][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.223][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.230][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:29.231][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:29.232][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.234][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.240][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:29.242][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-03-28 16:02:29.243][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.244][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.251][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:29.252][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-03-28 16:02:29.253][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.255][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:02:29.265][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.266][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-28 16:02:29.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.269][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:29.272][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-28 16:02:29.277][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-28 16:02:29.279][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:29.280][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:29.282][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:29.283][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:29.284][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:29.285][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:29.350][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.351][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-28 16:02:29.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.353][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:29.357][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:29.359][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:29.360][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.361][ef$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:29.363][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2026-03-28 16:02:29.374][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-03-28 16:02:29.376][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:29.377][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:29.379][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:29.380][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:29.381][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:29.383][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:29.384][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:29.441][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.442][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-28 16:02:29.443][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.444][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:29.454][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-03-28 16:02:29.455][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:29.457][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:29.458][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:29.460][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:29.461][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:29.462][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:29.464][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:29.526][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.528][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-28 16:02:29.529][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.530][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:29.535][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-03-28 16:02:29.536][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:29.538][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:29.540][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:29.541][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:29.542][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:29.543][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:29.545][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:29.602][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.604][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-28 16:02:29.605][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.606][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:29.670][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.671][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-28 16:02:29.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.674][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:29.731][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.732][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:29.734][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.735][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:29.793][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.794][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:29.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.797][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-03-28 16:02:29.871][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:29.872][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:29.873][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.875][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:29.876][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:29.877][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:29.879][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:29.880][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:02:29.882][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.883][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2026-03-28 16:02:29.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.886][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:29.896][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-03-28 16:02:29.898][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:29.900][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:29.901][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:29.902][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:29.904][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:29.905][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:29.907][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:29.966][biodb::testThat]
biodb.INFO [2026-03-28 16:02:29.967][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2026-03-28 16:02:29.969][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:29.970][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:29.973][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-28 16:02:29.975][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-28 16:02:29.977][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:29.978][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:29.979][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:29.981][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:29.982][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:29.983][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:30.046][biodb::testThat]
biodb.INFO [2026-03-28 16:02:30.048][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2026-03-28 16:02:30.049][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:30.050][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:30.054][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-28 16:02:30.055][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-28 16:02:30.057][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:30.058][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:30.060][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:30.061][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:30.062][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:30.064][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:30.122][biodb::testThat]
biodb.INFO [2026-03-28 16:02:30.124][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2026-03-28 16:02:30.125][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:30.126][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:30.130][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-28 16:02:30.131][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-28 16:02:30.133][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:30.135][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:30.136][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:30.138][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:30.139][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:30.140][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-03-28 16:02:30.205][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:30.207][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:30.208][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:30.209][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:30.211][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:30.212][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:30.213][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:30.214][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:02:30.216][biodb::testThat]
biodb.INFO [2026-03-28 16:02:30.218][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2026-03-28 16:02:30.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:30.220][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:30.224][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-28 16:02:30.225][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-28 16:02:30.227][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:30.229][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:30.230][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:30.231][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:30.232][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:30.234][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:30.293][biodb::testThat]
biodb.INFO [2026-03-28 16:02:30.294][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2026-03-28 16:02:30.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:30.297][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:30.301][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-03-28 16:02:30.302][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-03-28 16:02:30.304][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:30.305][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:30.307][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:30.308][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:30.309][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:30.311][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-03-28 16:02:30.376][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:02:30.377][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2026-03-28 16:02:30.379][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:02:30.380][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:30.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:30.382][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.385][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-28 16:02:30.393][biodb::testContext]
biodb.INFO [2026-03-28 16:02:30.394][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:30.396][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2026-03-28 16:02:30.397][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:30.399][biodb::testContext]
biodb.INFO [2026-03-28 16:02:30.401][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:30.404][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:30.409][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:30.411][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:02:30.412][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:02:30.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.416][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[2026-03-28 16:02:30.418][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:02:30.445][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:02:30.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:30.450][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:02:30.451][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:02:30.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.455][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[2026-03-28 16:02:30.457][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:02:30.458][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:02:30.459][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:02:30.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:30.465][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:02:30.466][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:02:30.467][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:02:30.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.471][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[2026-03-28 16:02:30.473][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:02:30.474][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:02:30.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:30.479][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:02:30.481][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:02:30.482][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:02:30.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.486][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[2026-03-28 16:02:30.487][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:02:30.489][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:02:30.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:30.493][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:02:30.494][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:02:30.500][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:02:30.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.504][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[2026-03-28 16:02:30.506][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:30.507][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:02:30.508][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:02:30.509][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:02:30.511][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:02:30.512][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:02:30.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:30.517][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:02:30.518][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:02:30.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.521][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[2026-03-28 16:02:30.523][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:02:30.524][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:02:30.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:30.529][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:02:30.530][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:02:30.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.533][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[2026-03-28 16:02:30.535][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:02:30.536][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:02:30.537][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:02:30.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:30.542][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:30.543][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:02:30.553][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:02:30.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.557][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[2026-03-28 16:02:30.558][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:02:30.559][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:02:30.561][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:02:30.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:30.566][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:02:30.568][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.569][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-28 16:02:30.570][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.572][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:30.573][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.574][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.575][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.577][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.578][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:30.579][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:30.581][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.582][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:02:30.583][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:30.584][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.586][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.587][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:30.587][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:30.587][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:30.587][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:30.587][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:30.588][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:30.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:30.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:30.592][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:30.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:30.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:30.596][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.597][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.598][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:30.599][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:30.600][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.602][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.603][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:02:30.606][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.607][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:30.608][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.609][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:30.611][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.612][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.613][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.616][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:30.617][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:30.618][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.620][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:02:30.621][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:30.622][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.623][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.625][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:30.625][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:30.625][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:30.625][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:30.625][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:30.626][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:30.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:30.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:30.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:30.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:30.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:30.633][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.635][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:30.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:30.638][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.639][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.641][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:02:30.643][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.644][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-28 16:02:30.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.647][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:30.648][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.650][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.651][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.653][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:30.655][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:30.656][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.657][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:02:30.659][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:30.660][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.661][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.662][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.664][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:30.665][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:30.666][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:30.668][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:30.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:30.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:30.671][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.673][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.674][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:30.675][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:30.676][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.682][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.683][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:02:30.686][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.687][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:30.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.690][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:30.691][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.692][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.694][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.696][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:30.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:30.699][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.700][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:02:30.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:30.702][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.704][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:30.705][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.706][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:30.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:30.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:30.710][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:30.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:30.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:30.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:30.715][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.716][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:30.717][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:30.718][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:30.720][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:30.721][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:30.722][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.724][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[2026-03-28 16:02:30.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.729][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[2026-03-28 16:02:30.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.735][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[2026-03-28 16:02:30.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.741][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[2026-03-28 16:02:30.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.747][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[2026-03-28 16:02:30.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.752][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[2026-03-28 16:02:30.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.758][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[2026-03-28 16:02:30.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.764][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[2026-03-28 16:02:30.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.770][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[2026-03-28 16:02:30.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.776][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[2026-03-28 16:02:30.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.781][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[2026-03-28 16:02:30.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.787][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[2026-03-28 16:02:30.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.793][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[2026-03-28 16:02:30.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.799][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[2026-03-28 16:02:30.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.804][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[2026-03-28 16:02:30.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.810][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[2026-03-28 16:02:30.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.816][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[2026-03-28 16:02:30.817][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:02:30.819][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:02:30.821][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:02:30.823][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:02:30.825][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:02:30.826][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:02:30.828][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:30.830][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:30.832][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:02:30.833][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:02:30.835][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:02:30.837][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:02:30.839][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:30.840][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:30.842][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:30.844][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:30.846][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:02:30.847][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:02:30.854][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:02:30.856][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:02:30.858][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:02:30.860][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:02:30.861][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:02:30.863][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:02:30.865][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:02:30.867][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:02:30.868][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:02:30.870][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:02:30.872][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:02:30.874][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:02:30.876][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:02:30.877][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:02:30.879][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:02:30.881][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:02:30.883][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:02:30.884][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:02:30.886][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:02:30.888][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:02:30.890][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:02:30.891][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:02:30.893][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:02:30.895][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:02:30.897][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:02:30.899][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:02:30.900][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:02:30.902][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:30.904][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:02:30.906][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:02:30.908][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:02:30.909][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:02:30.911][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:02:30.913][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:02:30.915][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:02:30.917][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:02:30.918][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:02:30.920][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:02:30.922][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:02:30.924][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:02:30.926][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:02:30.927][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:02:30.929][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:02:30.931][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:02:30.933][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:02:30.934][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:02:30.936][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:02:30.938][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:02:30.940][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:02:30.941][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:02:30.943][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:02:30.945][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:02:30.947][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:02:30.949][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:02:30.950][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:02:30.952][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:02:30.954][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:02:30.956][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:02:30.957][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:02:30.959][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:02:30.961][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:02:30.963][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:02:30.964][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:02:30.966][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:02:30.968][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:02:30.970][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:02:30.972][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:30.973][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:30.974][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.976][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.977][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[2026-03-28 16:02:30.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:30.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:30.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.985][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[2026-03-28 16:02:30.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:30.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:30.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:30.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:30.994][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[2026-03-28 16:02:30.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:30.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:30.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:30.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:30.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.002][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[2026-03-28 16:02:31.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.010][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[2026-03-28 16:02:31.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.027][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[2026-03-28 16:02:31.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.036][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[2026-03-28 16:02:31.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.044][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[2026-03-28 16:02:31.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.052][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[2026-03-28 16:02:31.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.060][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[2026-03-28 16:02:31.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.068][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[2026-03-28 16:02:31.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.076][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[2026-03-28 16:02:31.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.084][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[2026-03-28 16:02:31.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.093][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[2026-03-28 16:02:31.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.100][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[2026-03-28 16:02:31.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.109][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[2026-03-28 16:02:31.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:31.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.117][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[2026-03-28 16:02:31.119][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:31.122][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-03-28 16:02:31.124][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.125][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-03-28 16:02:31.127][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.128][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:31.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.131][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.132][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.134][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-03-28 16:02:31.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:31.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.138][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-03-28 16:02:31.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:31.141][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-03-28 16:02:31.141][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-03-28 16:02:31.142][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:31.144][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:31.145][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:31.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:31.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:31.149][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:31.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:31.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:31.152][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.154][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-03-28 16:02:31.154][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-03-28 16:02:31.155][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:31.156][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:31.157][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.159][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:31.160][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-03-28 16:02:31.163][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.164][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-03-28 16:02:31.165][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.167][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:31.168][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.169][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.171][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.172][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.173][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:31.174][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:31.176][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.177][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-03-28 16:02:31.178][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:31.180][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-03-28 16:02:31.180][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-03-28 16:02:31.180][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-03-28 16:02:31.180][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-03-28 16:02:31.180][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-03-28 16:02:31.180][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-03-28 16:02:31.181][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:31.182][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:31.184][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:31.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:31.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:31.187][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:31.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:31.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:31.191][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.192][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:31.192][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:31.194][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:31.195][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:31.196][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.198][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:31.199][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-03-28 16:02:31.207][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:31.209][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-03-28 16:02:31.210][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:31.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.217][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.218][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.220][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:31.221][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:31.222][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.224][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-03-28 16:02:31.225][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$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[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.226][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-03-28 16:02:31.228][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:31.229][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:31.229][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:31.229][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:31.231][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-28 16:02:31.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:31.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:31.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:31.235][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:31.237][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:31.238][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.239][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:31.239][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:31.239][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-28 16:02:31.240][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:31.242][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:31.243][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.244][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-28 16:02:31.246][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-28 16:02:31.248][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.249][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-03-28 16:02:31.251][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:31.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.255][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.256][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.257][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.258][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:31.260][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:31.261][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.262][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-03-28 16:02:31.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:31.265][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-03-28 16:02:31.265][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-03-28 16:02:31.266][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:31.267][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:31.269][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-03-28 16:02:31.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:31.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:31.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:31.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:31.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:31.276][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:31.277][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:31.277][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-03-28 16:02:31.277][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-03-28 16:02:31.278][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:31.279][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:31.281][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:31.282][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-03-28 16:02:31.284][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-03-28 16:02:31.285][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:31.287][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:31.289][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-03-28 16:02:31.291][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:31.293][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-03-28 16:02:31.300][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2026-03-28 16:02:31.305][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2026-03-28 16:02:31.310][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.312][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-28 16:02:31.313][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:31.314][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:31.317][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2026-03-28 16:02:31.319][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:31.322][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2026-03-28 16:02:31.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:31.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:31.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:31.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:31.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:31.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:31.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:31.340][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.341][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.342][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.343][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.350][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.351][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.353][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.354][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.355][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.361][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.366][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.376][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:31.419][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2026-03-28 16:02:31.422][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:31.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:31.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.428][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-03-28 16:02:31.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-03-28 16:02:31.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:31.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-03-28 16:02:31.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.438][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:31.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:31.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:31.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:31.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:31.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:31.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:31.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:31.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.472][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.515][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.520][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.525][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-03-28 16:02:31.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.554][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.555][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.556][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.557][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.581][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.586][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.596][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.598][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.599][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.600][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.617][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:31.619][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:31.620][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.621][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:31.628][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.629][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:31.630][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:31.631][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:02:31.642][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.643][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-28 16:02:31.644][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:31.645][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:31.648][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-03-28 16:02:31.654][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:31.656][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:31.657][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:31.658][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:31.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:31.661][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:31.662][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-28 16:02:31.720][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.721][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-28 16:02:31.723][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:31.724][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.732][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.734][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-28 16:02:31.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:31.736][biodb::testThat]
biodb.WARN [2026-03-28 16:02:31.745][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-03-28 16:02:31.749][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-03-28 16:02:31.760][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.762][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-28 16:02:31.763][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:31.764][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:31.769][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-03-28 16:02:31.770][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-03-28 16:02:31.772][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-03-28 16:02:31.774][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-03-28 16:02:31.775][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:31.776][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-03-28 16:02:31.778][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-03-28 16:02:31.779][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-28 16:02:31.838][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.840][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-28 16:02:31.841][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:31.842][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-28 16:02:31.907][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.909][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-28 16:02:31.910][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:31.911][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-28 16:02:31.971][biodb::testThat]
biodb.INFO [2026-03-28 16:02:31.972][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:31.973][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:31.975][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-28 16:02:32.035][biodb::testThat]
biodb.INFO [2026-03-28 16:02:32.036][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:32.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:32.039][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-03-28 16:02:32.104][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:02:32.106][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2026-03-28 16:02:32.107][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:02:32.108][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:32.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:32.111][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:32.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:32.113][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:32.114][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  8.1Mb
  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)