Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-14 23:55 -0500 (Sat, 14 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4889
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4679
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-02-14 09:55 -0500 (Sat, 14 Feb 2026)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

To the developers/maintainers of the biodbNci 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: biodbNci
Version: 1.14.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-02-14 16:02:16 -0500 (Sat, 14 Feb 2026)
EndedAt: 2026-02-14 16:03:19 -0500 (Sat, 14 Feb 2026)
EllapsedTime: 63.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.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-pc-linux-gnu

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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("biodbNci")
biodb.INFO [2026-02-14 16:03:15.927][biodb::testContext]
biodb.INFO [2026-02-14 16:03:15.928][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:03:15.929][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-14 16:03:15.930][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:03:15.931][biodb::testContext]
biodb.INFO [2026-02-14 16:03:15.937][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:03:15.938][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-02-14 16:03:15.945][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:03:15.946][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-14 16:03:15.947][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-14 16:03:15.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:15.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:15.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:15.950][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-14 16:03:15.966][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-14 16:03:15.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:15.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:15.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:15.970][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-14 16:03:15.970][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-14 16:03:15.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:15.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:15.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:15.974][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-14 16:03:15.975][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-14 16:03:15.976][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-14 16:03:15.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:15.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:15.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:15.979][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-14 16:03:15.980][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-14 16:03:15.981][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-14 16:03:15.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:15.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:15.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:15.984][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-14 16:03:15.985][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-14 16:03:15.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:15.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:15.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:15.989][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-14 16:03:15.990][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-14 16:03:15.990][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-14 16:03:15.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:15.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:15.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:15.994][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-14 16:03:15.995][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-14 16:03:15.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:15.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:15.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:15.998][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-14 16:03:15.999][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-14 16:03:16.000][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-14 16:03:16.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.003][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:03:16.004][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-14 16:03:16.005][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-14 16:03:16.006][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-14 16:03:16.007][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-14 16:03:16.008][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-14 16:03:16.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.010][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[2026-02-14 16:03:16.011][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-14 16:03:16.012][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-14 16:03:16.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.016][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-14 16:03:16.017][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-14 16:03:16.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.020][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-14 16:03:16.021][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-14 16:03:16.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.024][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-14 16:03:16.025][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-14 16:03:16.026][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-14 16:03:16.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.030][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:03:16.030][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-14 16:03:16.035][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-14 16:03:16.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.038][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-14 16:03:16.039][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-14 16:03:16.040][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-14 16:03:16.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.046][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-14 16:03:16.076][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.096][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-14 16:03:16.097][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.098][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:16.099][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.100][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.101][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.102][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.102][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:03:16.103][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:16.104][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.105][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-14 16:03:16.106][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:16.107][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.108][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.109][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:03:16.109][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:03:16.109][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:03:16.109][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:03:16.109][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:03:16.110][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:03:16.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.112][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:16.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.115][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.116][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.117][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:16.118][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:16.119][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.119][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.121][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-14 16:03:16.122][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.123][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:03:16.124][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.125][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:16.126][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.127][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.128][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.129][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.130][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:03:16.131][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:16.132][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.132][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-14 16:03:16.133][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:16.134][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.135][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.136][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:03:16.136][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:03:16.136][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:03:16.136][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:03:16.136][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:03:16.137][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:03:16.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.139][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.140][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:16.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.141][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.142][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.143][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.144][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:16.145][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:16.146][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.147][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.148][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-14 16:03:16.150][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.150][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-14 16:03:16.151][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.152][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:16.153][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.154][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.155][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.156][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.157][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:03:16.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:16.159][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.160][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-14 16:03:16.161][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:16.162][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.163][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.163][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.164][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:03:16.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.167][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:16.168][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.171][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.171][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:16.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:16.173][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.174][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.175][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-14 16:03:16.177][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.178][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:03:16.179][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.180][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:16.180][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.181][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.182][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.183][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.184][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:03:16.185][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:16.186][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.187][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-14 16:03:16.188][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:16.189][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.190][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.191][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.192][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:03:16.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.194][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:16.195][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.196][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.197][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.198][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.199][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:16.200][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:16.200][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.201][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.205][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:03:16.206][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.227][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[2026-02-14 16:03:16.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.274][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-14 16:03:16.278][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-14 16:03:16.279][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-14 16:03:16.280][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-14 16:03:16.282][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-14 16:03:16.283][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-14 16:03:16.284][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-14 16:03:16.285][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-14 16:03:16.287][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-14 16:03:16.288][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-14 16:03:16.293][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-14 16:03:16.295][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-14 16:03:16.296][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-14 16:03:16.297][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-14 16:03:16.298][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-14 16:03:16.300][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-14 16:03:16.301][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-14 16:03:16.302][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-14 16:03:16.303][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-14 16:03:16.305][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-14 16:03:16.306][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-14 16:03:16.307][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-14 16:03:16.314][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-14 16:03:16.317][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-14 16:03:16.318][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-14 16:03:16.320][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-14 16:03:16.321][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-14 16:03:16.323][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-14 16:03:16.325][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-14 16:03:16.326][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-14 16:03:16.328][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-14 16:03:16.329][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-14 16:03:16.331][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-14 16:03:16.332][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-14 16:03:16.334][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-14 16:03:16.335][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-14 16:03:16.337][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-14 16:03:16.338][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-14 16:03:16.340][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-14 16:03:16.341][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-14 16:03:16.342][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-14 16:03:16.344][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-14 16:03:16.345][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-14 16:03:16.347][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-14 16:03:16.348][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-14 16:03:16.350][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-14 16:03:16.351][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-14 16:03:16.353][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-14 16:03:16.354][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-14 16:03:16.356][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-14 16:03:16.357][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-14 16:03:16.359][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-14 16:03:16.360][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-14 16:03:16.362][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-14 16:03:16.363][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-14 16:03:16.364][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-14 16:03:16.366][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-14 16:03:16.367][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-14 16:03:16.369][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-14 16:03:16.370][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-14 16:03:16.372][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-14 16:03:16.373][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-14 16:03:16.374][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-14 16:03:16.376][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-14 16:03:16.377][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-14 16:03:16.379][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-14 16:03:16.380][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-14 16:03:16.382][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-14 16:03:16.383][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-14 16:03:16.384][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-14 16:03:16.386][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-14 16:03:16.387][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-14 16:03:16.389][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-14 16:03:16.390][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-14 16:03:16.392][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-14 16:03:16.393][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-14 16:03:16.394][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-14 16:03:16.396][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-14 16:03:16.397][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-14 16:03:16.399][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-14 16:03:16.400][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-14 16:03:16.402][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-14 16:03:16.403][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-14 16:03:16.410][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-14 16:03:16.412][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:03:16.415][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:03:16.416][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.418][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.449][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[2026-02-14 16:03:16.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.523][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[2026-02-14 16:03:16.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.529][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[2026-02-14 16:03:16.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:16.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:16.537][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-14 16:03:16.546][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-14 16:03:16.548][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.549][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-14 16:03:16.550][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.551][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:16.552][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.553][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-14 16:03:16.554][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.555][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.556][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-14 16:03:16.556][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:16.557][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.558][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-14 16:03:16.559][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:16.560][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-14 16:03:16.560][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-14 16:03:16.560][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-14 16:03:16.560][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-14 16:03:16.560][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-14 16:03:16.560][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-14 16:03:16.560][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-14 16:03:16.561][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:16.562][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.563][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-14 16:03:16.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:16.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:16.567][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:16.568][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:16.569][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-14 16:03:16.569][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-14 16:03:16.569][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-14 16:03:16.569][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-14 16:03:16.570][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:16.571][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:16.572][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:16.573][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:16.578][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-14 16:03:16.599][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-14 16:03:16.614][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-14 16:03:16.622][biodb::testThat]
biodb.INFO [2026-02-14 16:03:16.622][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-14 16:03:16.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:16.624][biodb::testThat]
biodb.TRACE[2026-02-14 16:03:16.627][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-02-14 16:03:16.629][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-14 16:03:16.632][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-14 16:03:16.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-14 16:03:16.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:16.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:16.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:16.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:16.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:16.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-14 16:03:16.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:16.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:16.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.720][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:16.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:16.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:16.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:16.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:16.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:16.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:16.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:16.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:16.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:16.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.758][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.761][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.769][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-14 16:03:16.827][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-02-14 16:03:16.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:03:16.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:03:16.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.833][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:03:16.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:03:16.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-14 16:03:16.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-14 16:03:16.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.840][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-14 16:03:16.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-14 16:03:16.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.860][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.895][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.899][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.903][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:16.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.923][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.924][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.925][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.926][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:16.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:16.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.938][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:16.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:16.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.946][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:16.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:16.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.949][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:16.950][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:16.951][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.952][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:16.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:16.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.975][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.976][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.977][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.978][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:16.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:16.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:16.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:16.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:16.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:16.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:16.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:16.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.001][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.002][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.003][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.003][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.026][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.027][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.029][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.041][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.042][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.043][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.044][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.047][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.049][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.049][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.050][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.058][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.059][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.060][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.061][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.065][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.066][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.067][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.068][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.072][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.073][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.073][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.074][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.090][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-02-14 16:03:17.123][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-14 16:03:17.124][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-14 16:03:17.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-14 16:03:17.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:17.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:17.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:17.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:17.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:17.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-14 16:03:17.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.167][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.171][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.273][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.277][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.284][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-14 16:03:17.310][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-02-14 16:03:17.329][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:03:17.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:03:17.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.333][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:03:17.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:03:17.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-14 16:03:17.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-14 16:03:17.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.340][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-14 16:03:17.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-14 16:03:17.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.352][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.383][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.386][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.390][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:03:17.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.423][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.424][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.425][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.426][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.438][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.442][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.445][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.449][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.450][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.451][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.452][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.453][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.474][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.475][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.476][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.477][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.499][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.500][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.501][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.502][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.525][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.526][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.526][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.527][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.550][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.551][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.551][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.552][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.578][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.579][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.580][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.581][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.592][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:03:17.593][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:03:17.594][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.595][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.599][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.600][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:03:17.601][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.602][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.606][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:03:17.606][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:03:17.607][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.608][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.612][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:03:17.613][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:03:17.614][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.615][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.619][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.620][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:03:17.621][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.621][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.625][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.626][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:03:17.627][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.628][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:03:17.632][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:03:17.633][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:03:17.634][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:03:17.635][ef$get] fields variable is a list.
biodb.INFO [2026-02-14 16:03:17.641][biodb::testThat]
biodb.INFO [2026-02-14 16:03:17.642][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-14 16:03:17.643][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:17.644][biodb::testThat]
biodb.DEBUG[2026-02-14 16:03:17.646][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-02-14 16:03:17.648][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-02-14 16:03:17.650][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-14 16:03:17.678][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-14 16:03:17.679][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-14 16:03:17.680][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-14 16:03:17.807][biodb::testThat]
biodb.INFO [2026-02-14 16:03:17.808][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-14 16:03:17.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:17.810][biodb::testThat]
biodb.INFO [2026-02-14 16:03:17.815][biodb::testThat]
biodb.INFO [2026-02-14 16:03:17.816][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-14 16:03:17.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:17.818][biodb::testThat]
biodb.WARN [2026-02-14 16:03:17.833][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-14 16:03:17.855][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-14 16:03:17.862][biodb::testThat]
biodb.INFO [2026-02-14 16:03:17.863][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-14 16:03:17.864][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:17.865][biodb::testThat]
biodb.DEBUG[2026-02-14 16:03:17.880][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-02-14 16:03:17.924][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-14 16:03:17.926][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-14 16:03:17.927][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-14 16:03:17.928][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-14 16:03:17.940][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-14 16:03:17.994][biodb::testThat]
biodb.INFO [2026-02-14 16:03:17.995][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-14 16:03:17.996][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:17.997][biodb::testThat]
biodb.INFO [2026-02-14 16:03:18.004][biodb::testThat]
biodb.INFO [2026-02-14 16:03:18.005][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-14 16:03:18.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:18.006][biodb::testThat]
biodb.INFO [2026-02-14 16:03:18.013][biodb::testThat]
biodb.INFO [2026-02-14 16:03:18.014][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-14 16:03:18.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:18.015][biodb::testThat]
biodb.INFO [2026-02-14 16:03:18.021][biodb::testThat]
biodb.INFO [2026-02-14 16:03:18.022][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-14 16:03:18.022][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:03:18.023][biodb::testThat]
biodb.INFO [2026-02-14 16:03:18.028][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-14 16:03:18.029][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-14 16:03:18.030][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-14 16:03:18.031][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.033][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.035][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-14 16:03:18.044][biodb::testContext]
biodb.INFO [2026-02-14 16:03:18.045][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:03:18.046][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-02-14 16:03:18.047][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:03:18.048][biodb::testContext]
biodb.INFO [2026-02-14 16:03:18.050][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:03:18.051][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-02-14 16:03:18.055][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:03:18.056][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-14 16:03:18.057][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-14 16:03:18.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.060][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-14 16:03:18.061][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-14 16:03:18.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.065][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-14 16:03:18.066][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-14 16:03:18.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.069][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-14 16:03:18.070][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-14 16:03:18.071][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-14 16:03:18.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.074][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-14 16:03:18.075][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-14 16:03:18.076][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-14 16:03:18.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.079][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-14 16:03:18.080][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-14 16:03:18.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.084][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-14 16:03:18.085][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-14 16:03:18.086][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-14 16:03:18.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.089][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-14 16:03:18.090][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-14 16:03:18.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.093][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-14 16:03:18.094][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-14 16:03:18.095][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-14 16:03:18.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.099][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:03:18.100][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-14 16:03:18.100][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-14 16:03:18.101][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-14 16:03:18.102][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-14 16:03:18.103][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-14 16:03:18.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.107][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-14 16:03:18.108][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-14 16:03:18.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.111][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-14 16:03:18.112][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-14 16:03:18.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.115][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-14 16:03:18.116][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-14 16:03:18.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.120][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-14 16:03:18.121][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-14 16:03:18.122][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-14 16:03:18.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.125][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:03:18.130][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-14 16:03:18.133][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-14 16:03:18.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.136][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-14 16:03:18.137][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-14 16:03:18.138][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-14 16:03:18.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.142][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-14 16:03:18.143][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.144][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-14 16:03:18.145][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.146][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:18.147][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.148][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.149][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.150][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.151][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:03:18.152][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:18.152][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.153][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-14 16:03:18.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:18.155][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.156][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.157][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:03:18.157][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:03:18.157][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:03:18.157][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:03:18.157][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:03:18.158][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:03:18.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.161][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:18.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.163][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.164][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.165][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:18.166][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:18.167][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.168][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.169][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-14 16:03:18.170][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.171][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:03:18.172][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.173][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:18.174][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.175][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.176][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.177][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.178][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:03:18.179][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:18.180][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.181][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-14 16:03:18.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:18.183][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.184][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.185][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:03:18.185][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:03:18.185][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:03:18.185][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:03:18.185][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:03:18.185][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:03:18.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.188][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:18.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.191][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.192][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.193][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:18.193][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:18.194][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.195][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.196][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-14 16:03:18.198][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.199][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-14 16:03:18.200][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.201][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:18.202][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.203][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.204][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.205][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.206][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:03:18.206][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:18.207][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.208][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-14 16:03:18.209][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:18.210][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.211][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.212][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.213][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:03:18.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.216][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:18.217][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.217][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.218][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.219][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.220][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:18.221][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:18.222][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.223][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.224][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-14 16:03:18.225][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.226][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:03:18.227][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.228][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:18.229][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.230][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.231][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.232][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.233][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:03:18.234][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:18.235][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.236][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-14 16:03:18.237][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:18.238][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.239][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.240][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.241][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:03:18.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.243][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:18.244][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.245][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.246][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.247][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.248][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:18.248][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:18.249][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.250][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.252][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:03:18.252][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.270][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[2026-02-14 16:03:18.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.311][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[2026-02-14 16:03:18.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.324][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-14 16:03:18.325][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-14 16:03:18.327][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-14 16:03:18.328][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-14 16:03:18.329][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-14 16:03:18.331][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-14 16:03:18.332][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-14 16:03:18.333][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-14 16:03:18.335][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-14 16:03:18.336][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-14 16:03:18.337][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-14 16:03:18.338][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-14 16:03:18.340][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-14 16:03:18.341][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-14 16:03:18.342][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-14 16:03:18.344][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-14 16:03:18.345][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-14 16:03:18.346][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-14 16:03:18.348][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-14 16:03:18.349][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-14 16:03:18.350][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-14 16:03:18.351][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-14 16:03:18.353][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-14 16:03:18.354][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-14 16:03:18.355][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-14 16:03:18.357][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-14 16:03:18.358][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-14 16:03:18.359][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-14 16:03:18.360][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-14 16:03:18.362][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-14 16:03:18.363][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-14 16:03:18.364][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-14 16:03:18.366][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-14 16:03:18.367][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-14 16:03:18.368][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-14 16:03:18.370][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-14 16:03:18.371][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-14 16:03:18.372][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-14 16:03:18.373][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-14 16:03:18.375][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-14 16:03:18.376][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-14 16:03:18.377][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-14 16:03:18.379][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-14 16:03:18.380][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-14 16:03:18.381][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-14 16:03:18.382][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-14 16:03:18.384][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-14 16:03:18.385][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-14 16:03:18.386][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-14 16:03:18.388][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-14 16:03:18.389][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-14 16:03:18.390][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-14 16:03:18.392][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-14 16:03:18.393][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-14 16:03:18.394][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-14 16:03:18.395][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-14 16:03:18.397][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-14 16:03:18.398][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-14 16:03:18.399][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-14 16:03:18.401][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-14 16:03:18.402][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-14 16:03:18.403][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-14 16:03:18.405][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-14 16:03:18.406][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-14 16:03:18.407][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-14 16:03:18.408][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-14 16:03:18.410][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-14 16:03:18.411][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-14 16:03:18.412][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-14 16:03:18.414][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-14 16:03:18.415][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-14 16:03:18.416][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-14 16:03:18.417][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-14 16:03:18.419][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-14 16:03:18.420][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-14 16:03:18.421][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-14 16:03:18.423][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-14 16:03:18.428][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-14 16:03:18.430][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-14 16:03:18.431][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-14 16:03:18.432][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-14 16:03:18.433][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-14 16:03:18.435][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-14 16:03:18.436][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-14 16:03:18.437][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:03:18.438][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:03:18.439][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.441][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.453][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[2026-02-14 16:03:18.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.477][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[2026-02-14 16:03:18.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:03:18.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:03:18.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.535][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[2026-02-14 16:03:18.537][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-14 16:03:18.538][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-14 16:03:18.540][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.541][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-14 16:03:18.542][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.543][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:03:18.544][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.545][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-14 16:03:18.546][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.547][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.548][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-14 16:03:18.548][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:03:18.549][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.550][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-14 16:03:18.551][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:03:18.552][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-14 16:03:18.552][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-14 16:03:18.552][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-14 16:03:18.552][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-14 16:03:18.552][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-14 16:03:18.552][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-14 16:03:18.552][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-14 16:03:18.553][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-14 16:03:18.554][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.555][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-14 16:03:18.556][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.558][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:03:18.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:03:18.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:03:18.560][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:03:18.561][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-14 16:03:18.561][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-14 16:03:18.561][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-14 16:03:18.561][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-14 16:03:18.562][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:03:18.563][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:03:18.564][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-14 16:03:18.565][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:03:18.566][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-14 16:03:18.569][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-14 16:03:18.577][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-14 16:03:18.578][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-14 16:03:18.579][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-14 16:03:18.580][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-14 16:03:18.580][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:03:18.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:03:18.582][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:03:18.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:03:18.584][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:03:18.585][FUN] Functions in observer 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 2 | WARN 0 | SKIP 2 | PASS 85 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): ,

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, 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$getEntryContent(ids)
 8.             └─self$download()
 9.               └─private$doExtractDownload()

[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ 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 ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... 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:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, 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$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** 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 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)