Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-28 23:55 -0500 (Sat, 28 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4891
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4681
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/31HostnameOS / ArchCHECK
biodbNcbi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-02-28 09:55 -0500 (Sat, 28 Feb 2026)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: RELEASE_3_22
git_last_commit: dc1f90a
git_last_commit_date: 2025-10-29 11:15:40 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on merida1

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

raw results


Summary

Package: biodbNcbi
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
StartedAt: 2026-02-28 16:01:22 -0500 (Sat, 28 Feb 2026)
EndedAt: 2026-02-28 16:02:40 -0500 (Sat, 28 Feb 2026)
EllapsedTime: 77.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


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

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Type 'license()' or 'licence()' for distribution details.

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2026-02-28 16:02:27.456][biodb::testContext]
biodb.INFO [2026-02-28 16:02:27.459][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:27.461][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2026-02-28 16:02:27.462][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:27.463][biodb::testContext]
biodb.INFO [2026-02-28 16:02:27.470][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:27.472][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:27.479][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:27.481][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-28 16:02:27.482][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-28 16:02:27.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.487][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-28 16:02:27.511][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-28 16:02:27.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.516][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-28 16:02:27.517][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-28 16:02:27.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.522][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-28 16:02:27.523][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-28 16:02:27.525][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-28 16:02:27.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.529][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-28 16:02:27.530][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-28 16:02:27.532][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-28 16:02:27.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.536][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-28 16:02:27.538][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-28 16:02:27.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.542][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-28 16:02:27.543][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-28 16:02:27.545][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-28 16:02:27.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.549][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-28 16:02:27.551][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-28 16:02:27.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.555][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-28 16:02:27.557][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-28 16:02:27.558][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-28 16:02:27.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.563][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:27.564][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-28 16:02:27.565][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-28 16:02:27.566][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-28 16:02:27.568][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-28 16:02:27.569][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-28 16:02:27.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.574][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-28 16:02:27.575][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-28 16:02:27.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.580][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-28 16:02:27.581][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-28 16:02:27.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.585][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".
biodb.DEBUG[2026-02-28 16:02:27.586][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-28 16:02:27.587][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-28 16:02:27.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.592][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-28 16:02:27.593][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-28 16:02:27.594][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-28 16:02:27.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.599][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:27.600][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-28 16:02:27.610][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-28 16:02:27.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.615][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-28 16:02:27.616][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-28 16:02:27.618][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-28 16:02:27.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.625][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-28 16:02:27.667][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.695][self$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[2026-02-28 16:02:27.696][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.697][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:27.699][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.700][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.701][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.702][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.704][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:27.705][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:27.706][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.707][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-28 16:02:27.708][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:27.710][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.711][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.712][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:27.712][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:27.712][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:27.712][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:27.712][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:27.713][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:27.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:27.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:27.717][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:27.718][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:27.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:27.721][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.722][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.723][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:27.724][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:27.725][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.727][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.728][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-28 16:02:27.730][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.731][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:27.733][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.734][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:27.735][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.736][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.738][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.739][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.740][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:27.741][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:27.743][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.744][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-28 16:02:27.745][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:27.746][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.747][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.749][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:27.749][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:27.749][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:27.749][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:27.749][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:27.750][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:27.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:27.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:27.753][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:27.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:27.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:27.757][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.758][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.759][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:27.761][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:27.762][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.763][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.765][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-28 16:02:27.767][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.768][self$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[2026-02-28 16:02:27.769][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.770][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:27.772][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.773][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.774][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.777][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:27.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:27.779][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.780][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-28 16:02:27.782][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:27.783][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.784][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.785][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.787][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:27.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:27.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:27.790][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:27.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:27.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:27.794][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.795][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.796][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:27.797][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:27.799][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.800][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.801][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-28 16:02:27.804][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.805][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:27.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:27.809][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.810][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.811][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.812][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.813][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:27.815][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:27.816][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.817][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-28 16:02:27.818][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:27.820][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.821][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:27.822][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.823][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:27.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:27.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:27.827][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:27.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:27.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:27.830][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:27.831][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.833][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:27.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:27.835][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:27.836][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:27.840][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:27.841][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:27.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:27.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:27.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:27.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:27.934][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-28 16:02:27.943][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-28 16:02:27.945][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-28 16:02:27.947][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-28 16:02:27.949][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-28 16:02:27.951][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-28 16:02:27.952][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:27.954][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:27.956][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-28 16:02:27.958][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-28 16:02:27.959][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-28 16:02:27.961][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-28 16:02:27.963][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:27.964][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:27.966][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:27.968][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:27.969][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-28 16:02:27.971][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-28 16:02:27.973][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-28 16:02:27.975][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-28 16:02:27.976][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-28 16:02:27.978][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-28 16:02:27.980][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-28 16:02:27.981][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-28 16:02:27.983][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-28 16:02:27.985][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-28 16:02:27.987][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-28 16:02:27.988][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-28 16:02:27.990][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-28 16:02:27.992][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-28 16:02:27.993][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-28 16:02:27.995][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-28 16:02:27.997][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-28 16:02:27.998][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-28 16:02:28.000][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-28 16:02:28.002][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-28 16:02:28.004][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-28 16:02:28.005][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-28 16:02:28.007][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-28 16:02:28.009][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-28 16:02:28.010][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-28 16:02:28.012][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-28 16:02:28.014][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-28 16:02:28.016][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-28 16:02:28.017][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-28 16:02:28.019][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:28.021][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-28 16:02:28.023][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-28 16:02:28.024][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-28 16:02:28.026][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-28 16:02:28.028][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-28 16:02:28.029][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-28 16:02:28.031][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-28 16:02:28.033][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-28 16:02:28.035][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-28 16:02:28.036][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-28 16:02:28.038][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-28 16:02:28.040][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-28 16:02:28.041][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-28 16:02:28.043][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-28 16:02:28.045][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-28 16:02:28.047][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-28 16:02:28.048][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-28 16:02:28.050][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-28 16:02:28.052][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-28 16:02:28.054][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-28 16:02:28.055][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-28 16:02:28.057][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-28 16:02:28.059][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-28 16:02:28.060][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-28 16:02:28.062][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-28 16:02:28.064][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-28 16:02:28.066][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-28 16:02:28.067][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-28 16:02:28.069][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-28 16:02:28.071][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-28 16:02:28.073][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-28 16:02:28.074][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-28 16:02:28.076][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-28 16:02:28.078][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-28 16:02:28.080][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-28 16:02:28.081][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-28 16:02:28.083][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-28 16:02:28.091][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-28 16:02:28.093][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:28.096][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:28.097][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.100][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.114][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[2026-02-28 16:02:28.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:28.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:28.240][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:28.253][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-28 16:02:28.255][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.256][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-28 16:02:28.258][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.259][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:28.260][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.261][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.263][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.264][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.265][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-28 16:02:28.266][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:28.268][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.269][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-28 16:02:28.270][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:28.272][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-28 16:02:28.272][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-28 16:02:28.273][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:28.274][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:28.275][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:28.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:28.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:28.279][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:28.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:28.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:28.283][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.284][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-28 16:02:28.284][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-28 16:02:28.285][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:28.286][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:28.287][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.289][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:28.290][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-28 16:02:28.292][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.294][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-28 16:02:28.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:28.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.299][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.300][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.301][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.302][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:28.304][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:28.305][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.306][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-28 16:02:28.307][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:28.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-28 16:02:28.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-28 16:02:28.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-28 16:02:28.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-28 16:02:28.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-28 16:02:28.309][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-28 16:02:28.310][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:28.311][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:28.313][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:28.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:28.315][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:28.316][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:28.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:28.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:28.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.321][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:28.321][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:28.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:28.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:28.324][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.326][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:28.327][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-28 16:02:28.330][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:28.331][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-28 16:02:28.332][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.334][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:28.335][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.336][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.337][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.339][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.340][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:28.341][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:28.342][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.344][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-28 16:02:28.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.346][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:28.348][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:28.349][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:28.349][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:28.349][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:28.350][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-28 16:02:28.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:28.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:28.354][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:28.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:28.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:28.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.359][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:28.359][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:28.359][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-28 16:02:28.360][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:28.361][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:28.363][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.364][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-28 16:02:28.366][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-28 16:02:28.368][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.369][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-28 16:02:28.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.372][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:28.373][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.376][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.378][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:28.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:28.381][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.382][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-28 16:02:28.383][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:28.384][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-28 16:02:28.384][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-28 16:02:28.386][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:28.387][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:28.388][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-28 16:02:28.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:28.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:28.392][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:28.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:28.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:28.395][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:28.396][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:28.396][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:28.396][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-28 16:02:28.398][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:28.399][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:28.400][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:28.401][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-28 16:02:28.409][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-28 16:02:28.411][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:28.413][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:28.415][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-28 16:02:28.417][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:28.418][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-28 16:02:28.439][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-02-28 16:02:28.455][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2026-02-28 16:02:28.471][biodb::testThat]
biodb.INFO [2026-02-28 16:02:28.472][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-28 16:02:28.473][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:28.475][biodb::testThat]
biodb.TRACE[2026-02-28 16:02:28.479][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2026-02-28 16:02:28.481][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-02-28 16:02:28.485][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-02-28 16:02:28.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-28 16:02:28.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:28.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:28.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:28.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:28.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:28.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-28 16:02:28.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.556][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:28.574][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.575][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.576][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.613][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:28.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.619][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.624][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.634][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:28.724][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2026-02-28 16:02:28.727][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.732][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.769][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:28.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:28.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.774][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:28.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:28.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.779][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:28.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:28.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.784][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:28.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:28.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.811][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.855][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.860][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.865][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:28.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.895][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.897][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.898][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.916][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.921][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.931][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.936][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:28.937][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.939][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.940][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.941][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:28.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.956][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.958][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:28.959][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.960][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.966][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:28.968][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:28.969][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:28.970][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:28.993][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2026-02-28 16:02:29.041][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-02-28 16:02:29.043][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-02-28 16:02:29.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-28 16:02:29.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:29.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:29.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:29.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:29.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:29.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-28 16:02:29.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.100][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:29.102][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.103][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.104][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.106][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:29.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.111][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.116][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.126][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:29.197][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2026-02-28 16:02:29.225][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.230][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:29.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:29.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.241][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:29.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:29.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.246][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:29.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:29.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:29.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:29.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.267][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.313][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.323][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:29.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.364][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.366][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.367][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.368][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.385][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:29.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.394][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.399][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.404][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:29.406][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.407][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.408][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.409][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-02-28 16:02:29.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.425][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.427][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:29.428][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.429][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:29.435][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:29.437][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:29.438][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:29.439][ef$get] fields variable is a list.
biodb.INFO [2026-02-28 16:02:29.450][biodb::testThat]
biodb.INFO [2026-02-28 16:02:29.451][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-28 16:02:29.452][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:29.453][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:29.456][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2026-02-28 16:02:29.461][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2026-02-28 16:02:29.465][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-28 16:02:29.467][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:29.468][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-28 16:02:29.469][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:29.470][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-28 16:02:29.654][biodb::testThat]
biodb.INFO [2026-02-28 16:02:29.656][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-28 16:02:29.657][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:29.658][biodb::testThat]
biodb.INFO [2026-02-28 16:02:29.667][biodb::testThat]
biodb.INFO [2026-02-28 16:02:29.668][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-28 16:02:29.669][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:29.671][biodb::testThat]
biodb.WARN [2026-02-28 16:02:29.693][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-28 16:02:29.718][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-28 16:02:29.729][biodb::testThat]
biodb.INFO [2026-02-28 16:02:29.730][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-28 16:02:29.731][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:29.733][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:29.756][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2026-02-28 16:02:29.828][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:29.870][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-28 16:02:29.871][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:29.873][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-28 16:02:29.874][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:29.875][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-28 16:02:29.967][biodb::testThat]
biodb.INFO [2026-02-28 16:02:29.968][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-28 16:02:29.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:29.971][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-28 16:02:30.034][biodb::testThat]
biodb.INFO [2026-02-28 16:02:30.035][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-28 16:02:30.037][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:30.038][biodb::testThat]
biodb.INFO [2026-02-28 16:02:30.048][biodb::testThat]
biodb.INFO [2026-02-28 16:02:30.049][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:30.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:30.052][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-02-28 16:02:30.111][biodb::testThat]
biodb.INFO [2026-02-28 16:02:30.113][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:30.114][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:30.115][biodb::testThat]
biodb.INFO [2026-02-28 16:02:30.123][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-28 16:02:30.125][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-02-28 16:02:30.126][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-28 16:02:30.127][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.129][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.132][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-28 16:02:30.146][biodb::testContext]
biodb.INFO [2026-02-28 16:02:30.148][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:30.149][biodb::testContext] Test context - Gene long tests
biodb.INFO [2026-02-28 16:02:30.150][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:30.151][biodb::testContext]
biodb.INFO [2026-02-28 16:02:30.154][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:30.156][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:30.160][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:30.161][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-28 16:02:30.163][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-28 16:02:30.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.167][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-28 16:02:30.173][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-28 16:02:30.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.178][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-28 16:02:30.179][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-28 16:02:30.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.184][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-28 16:02:30.185][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-28 16:02:30.186][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-28 16:02:30.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.191][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-28 16:02:30.192][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-28 16:02:30.194][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-28 16:02:30.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.198][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-28 16:02:30.199][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-28 16:02:30.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.204][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-28 16:02:30.205][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-28 16:02:30.206][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-28 16:02:30.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.211][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-28 16:02:30.212][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-28 16:02:30.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.217][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-28 16:02:30.218][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-28 16:02:30.219][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-28 16:02:30.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.223][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[2026-02-28 16:02:30.224][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:30.225][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-28 16:02:30.226][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-28 16:02:30.228][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-28 16:02:30.229][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-28 16:02:30.230][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-28 16:02:30.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.235][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-28 16:02:30.236][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-28 16:02:30.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.240][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[2026-02-28 16:02:30.241][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-28 16:02:30.242][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-28 16:02:30.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.247][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-28 16:02:30.248][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-28 16:02:30.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.253][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-28 16:02:30.254][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-28 16:02:30.255][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-28 16:02:30.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.260][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:30.261][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-28 16:02:30.271][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-28 16:02:30.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.276][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-28 16:02:30.277][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-28 16:02:30.279][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-28 16:02:30.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.283][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-28 16:02:30.285][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.287][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-28 16:02:30.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.289][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:30.290][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.293][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.295][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:30.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:30.298][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.299][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-28 16:02:30.300][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:30.302][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.303][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.304][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:30.304][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:30.304][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:30.304][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:30.304][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:30.305][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:30.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:30.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.312][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.314][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.315][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:30.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:30.317][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.318][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.320][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-28 16:02:30.322][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.323][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:30.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:30.327][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.328][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.329][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.331][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.332][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:30.333][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:30.334][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.336][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-28 16:02:30.337][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:30.338][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.339][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.341][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:30.341][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:30.341][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:30.341][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:30.341][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:30.342][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:30.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.346][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:30.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.349][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.350][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.351][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:30.353][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:30.354][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.355][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.357][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-28 16:02:30.359][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.360][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-28 16:02:30.361][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.362][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:30.364][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.366][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.369][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:30.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:30.371][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.372][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-28 16:02:30.377][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:30.379][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.380][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.381][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.382][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:30.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.386][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:30.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.389][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.391][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:30.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:30.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.395][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.397][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-28 16:02:30.399][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.400][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:30.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.403][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:30.404][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.405][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.406][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.408][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.409][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:30.410][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:30.411][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.413][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-28 16:02:30.414][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:30.415][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.416][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.418][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.419][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:30.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.422][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:30.424][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.425][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.426][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.427][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.428][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:30.430][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:30.431][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.432][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.434][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:30.435][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.436][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[2026-02-28 16:02:30.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.442][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[2026-02-28 16:02:30.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.448][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[2026-02-28 16:02:30.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.453][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[2026-02-28 16:02:30.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.465][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[2026-02-28 16:02:30.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.477][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[2026-02-28 16:02:30.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.483][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[2026-02-28 16:02:30.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.500][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[2026-02-28 16:02:30.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.506][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[2026-02-28 16:02:30.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.512][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[2026-02-28 16:02:30.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.518][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[2026-02-28 16:02:30.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.523][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[2026-02-28 16:02:30.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.529][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[2026-02-28 16:02:30.530][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-28 16:02:30.532][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-28 16:02:30.534][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-28 16:02:30.536][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-28 16:02:30.537][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-28 16:02:30.539][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-28 16:02:30.541][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:30.542][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:30.544][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-28 16:02:30.546][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-28 16:02:30.548][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-28 16:02:30.549][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-28 16:02:30.551][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:30.553][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:30.555][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:30.556][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:30.558][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-28 16:02:30.560][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-28 16:02:30.561][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-28 16:02:30.563][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-28 16:02:30.565][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-28 16:02:30.567][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-28 16:02:30.568][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-28 16:02:30.574][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-28 16:02:30.576][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-28 16:02:30.578][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-28 16:02:30.580][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-28 16:02:30.581][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-28 16:02:30.583][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-28 16:02:30.585][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-28 16:02:30.586][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-28 16:02:30.588][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-28 16:02:30.590][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-28 16:02:30.592][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-28 16:02:30.593][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-28 16:02:30.595][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-28 16:02:30.597][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-28 16:02:30.598][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-28 16:02:30.600][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-28 16:02:30.602][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-28 16:02:30.604][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-28 16:02:30.605][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-28 16:02:30.607][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-28 16:02:30.609][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-28 16:02:30.612][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-28 16:02:30.614][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:30.616][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-28 16:02:30.617][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-28 16:02:30.619][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-28 16:02:30.621][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-28 16:02:30.623][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-28 16:02:30.624][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-28 16:02:30.626][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-28 16:02:30.628][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-28 16:02:30.630][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-28 16:02:30.631][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-28 16:02:30.633][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-28 16:02:30.635][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-28 16:02:30.636][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-28 16:02:30.638][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-28 16:02:30.640][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-28 16:02:30.642][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-28 16:02:30.643][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-28 16:02:30.645][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-28 16:02:30.647][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-28 16:02:30.649][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-28 16:02:30.650][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-28 16:02:30.652][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-28 16:02:30.654][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-28 16:02:30.656][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-28 16:02:30.657][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-28 16:02:30.659][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-28 16:02:30.661][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-28 16:02:30.663][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-28 16:02:30.664][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-28 16:02:30.666][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-28 16:02:30.668][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-28 16:02:30.670][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-28 16:02:30.671][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-28 16:02:30.673][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-28 16:02:30.675][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-28 16:02:30.677][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-28 16:02:30.678][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-28 16:02:30.680][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-28 16:02:30.682][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:30.683][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:30.685][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.687][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:30.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:30.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:30.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:30.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:30.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:30.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:30.834][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:30.836][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-28 16:02:30.839][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.840][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-28 16:02:30.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.843][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:30.844][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.845][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.847][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.848][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.849][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-28 16:02:30.850][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:30.852][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.853][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-28 16:02:30.854][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:30.856][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-28 16:02:30.856][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-28 16:02:30.857][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.858][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.859][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:30.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.863][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:30.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.865][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.866][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.868][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-28 16:02:30.868][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-28 16:02:30.869][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:30.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:30.871][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.873][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.874][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-28 16:02:30.877][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.878][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-28 16:02:30.879][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.880][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:30.882][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.883][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.884][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.886][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.887][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:30.888][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:30.889][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.891][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-28 16:02:30.892][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:30.894][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-28 16:02:30.894][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-28 16:02:30.894][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-28 16:02:30.894][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-28 16:02:30.894][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-28 16:02:30.894][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-28 16:02:30.895][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.896][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:30.898][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:30.899][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.901][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:30.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.905][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.906][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:30.906][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:30.907][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:30.909][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:30.910][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.911][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.913][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-28 16:02:30.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.917][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-28 16:02:30.918][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:30.920][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.922][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.923][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.925][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:30.927][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:30.928][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.929][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-28 16:02:30.931][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.932][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:30.934][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.935][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:30.935][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:30.935][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:30.936][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-28 16:02:30.938][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.940][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:30.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.945][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:30.945][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:30.945][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-28 16:02:30.946][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:30.947][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:30.949][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.950][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-28 16:02:30.952][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-28 16:02:30.954][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.956][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-28 16:02:30.957][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.958][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:30.959][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.962][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.963][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.965][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:30.966][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:30.967][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.969][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-28 16:02:30.970][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:30.971][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-28 16:02:30.971][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-28 16:02:30.973][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:30.974][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:30.975][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-28 16:02:30.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.983][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.984][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:30.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:30.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:30.988][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:30.989][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:30.989][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:30.989][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-28 16:02:30.991][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:30.992][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:30.993][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:30.995][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-28 16:02:30.997][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-28 16:02:30.998][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:31.001][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:31.003][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-28 16:02:31.005][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:31.007][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-28 16:02:31.016][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2026-02-28 16:02:31.059][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2026-02-28 16:02:31.065][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.066][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-28 16:02:31.067][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.069][biodb::testThat]
biodb.TRACE[2026-02-28 16:02:31.074][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2026-02-28 16:02:31.076][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2026-02-28 16:02:31.080][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2026-02-28 16:02:31.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-28 16:02:31.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:31.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:31.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:31.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:31.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:31.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-28 16:02:31.113][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.115][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.116][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.118][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.127][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:31.128][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:31.130][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.131][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.133][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:31.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:31.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.139][ef$get] Asked field names are: location.
biodb.TRACE[2026-02-28 16:02:31.140][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-02-28 16:02:31.142][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.143][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.145][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2026-02-28 16:02:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-02-28 16:02:31.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.151][ef$get] Asked field names are: symbol.
biodb.TRACE[2026-02-28 16:02:31.152][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-02-28 16:02:31.153][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.155][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.157][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2026-02-28 16:02:31.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-02-28 16:02:31.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.162][ef$get] Asked field names are: synonyms.
biodb.TRACE[2026-02-28 16:02:31.163][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:31.164][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.166][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.168][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2026-02-28 16:02:31.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:31.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.173][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-02-28 16:02:31.174][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-02-28 16:02:31.176][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.177][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.179][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-02-28 16:02:31.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-02-28 16:02:31.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.189][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:31.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:31.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-28 16:02:31.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-28 16:02:31.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.200][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-28 16:02:31.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-28 16:02:31.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.211][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-02-28 16:02:31.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-02-28 16:02:31.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:31.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:31.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:31.253][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2026-02-28 16:02:31.255][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.260][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:31.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:31.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.265][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:31.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:31.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.270][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:31.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:31.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:31.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:31.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:31.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:31.280][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2026-02-28 16:02:31.325][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-02-28 16:02:31.346][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2026-02-28 16:02:31.347][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2026-02-28 16:02:31.352][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:31.354][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-02-28 16:02:31.356][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:31.357][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-28 16:02:31.358][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:31.360][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-28 16:02:31.424][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.425][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-28 16:02:31.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.428][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:31.431][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2026-02-28 16:02:31.432][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2026-02-28 16:02:31.434][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-28 16:02:31.435][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:31.437][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:31.438][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:31.439][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:31.440][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-28 16:02:31.499][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.500][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-28 16:02:31.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.503][biodb::testThat]
biodb.TRACE[2026-02-28 16:02:31.507][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:31.508][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:31.509][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:31.510][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:31.512][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2026-02-28 16:02:31.524][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-28 16:02:31.525][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:31.527][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-28 16:02:31.529][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:31.530][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:31.531][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:31.532][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:31.557][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-28 16:02:31.641][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.642][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-28 16:02:31.643][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.645][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:31.655][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-28 16:02:31.656][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:31.658][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-28 16:02:31.659][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:31.660][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:31.662][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:31.663][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:31.664][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-28 16:02:31.724][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.725][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-28 16:02:31.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.728][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:31.733][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-02-28 16:02:31.735][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:31.737][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-02-28 16:02:31.738][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:31.740][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:31.741][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:31.742][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:31.743][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-28 16:02:31.807][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.808][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-28 16:02:31.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.811][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-28 16:02:31.869][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.872][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-28 16:02:31.874][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.876][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.889][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.890][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:31.891][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.892][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-02-28 16:02:31.956][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.957][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:31.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:31.960][biodb::testThat]
biodb.INFO [2026-02-28 16:02:31.968][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-28 16:02:31.969][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2026-02-28 16:02:31.971][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-02-28 16:02:31.972][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-28 16:02:31.973][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:31.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:31.975][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:31.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:31.977][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:31.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-28 16:02:31.983][biodb::testContext]
biodb.INFO [2026-02-28 16:02:31.984][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:31.985][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2026-02-28 16:02:31.987][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:31.988][biodb::testContext]
biodb.INFO [2026-02-28 16:02:31.990][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:31.992][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:31.996][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:31.997][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-28 16:02:31.999][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-28 16:02:32.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.002][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[2026-02-28 16:02:32.003][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-28 16:02:32.005][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-28 16:02:32.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.012][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-28 16:02:32.015][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-28 16:02:32.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.023][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[2026-02-28 16:02:32.025][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-28 16:02:32.027][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-28 16:02:32.030][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-28 16:02:32.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.039][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-28 16:02:32.042][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-28 16:02:32.045][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-28 16:02:32.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.054][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-28 16:02:32.056][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-28 16:02:32.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.065][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-28 16:02:32.067][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-28 16:02:32.070][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-28 16:02:32.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.078][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-28 16:02:32.081][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-28 16:02:32.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.090][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-28 16:02:32.092][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-28 16:02:32.094][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-28 16:02:32.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.102][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:32.104][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-28 16:02:32.106][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-28 16:02:32.109][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-28 16:02:32.111][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-28 16:02:32.114][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-28 16:02:32.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.121][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-28 16:02:32.122][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-28 16:02:32.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.129][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-28 16:02:32.132][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-28 16:02:32.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.138][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-28 16:02:32.139][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-28 16:02:32.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.145][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-28 16:02:32.146][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-28 16:02:32.148][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-28 16:02:32.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.152][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:32.153][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-28 16:02:32.164][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-28 16:02:32.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.168][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-28 16:02:32.170][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-28 16:02:32.171][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-28 16:02:32.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.181][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-28 16:02:32.183][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.184][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-28 16:02:32.185][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.186][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:32.188][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.189][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.190][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.191][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.193][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:32.194][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:32.195][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.196][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-28 16:02:32.198][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:32.199][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.200][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.201][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:32.201][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:32.201][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:32.201][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:32.201][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:32.203][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:32.204][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.206][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:32.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.209][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.210][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.211][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.212][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:32.213][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:32.215][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.216][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.217][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-28 16:02:32.220][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.221][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:32.222][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.223][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:32.225][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.226][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.227][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.228][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.230][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:32.231][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:32.232][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.233][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-28 16:02:32.235][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:32.236][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.237][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.238][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:32.238][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:32.238][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:32.238][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:32.238][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:32.240][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:32.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.243][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:32.244][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.245][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.247][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.248][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.249][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:32.250][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:32.251][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.253][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.254][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-28 16:02:32.256][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.257][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-28 16:02:32.259][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.260][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:32.261][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.262][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.264][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.265][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.266][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:32.267][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:32.269][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.270][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-28 16:02:32.271][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:32.272][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.273][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.275][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.276][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:32.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.279][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:32.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.283][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.284][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.285][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:32.286][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:32.288][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.289][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.290][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-28 16:02:32.292][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.294][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:32.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:32.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.299][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.300][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.301][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.302][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:32.304][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:32.305][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.306][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-28 16:02:32.307][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:32.309][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.310][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.311][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.312][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:32.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.315][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.316][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:32.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.319][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.321][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:32.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:32.324][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.326][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.327][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:32.328][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.425][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-28 16:02:32.427][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-28 16:02:32.429][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-28 16:02:32.430][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-28 16:02:32.432][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-28 16:02:32.434][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-28 16:02:32.436][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:32.438][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:32.439][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-28 16:02:32.441][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-28 16:02:32.443][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-28 16:02:32.445][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-28 16:02:32.447][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:32.449][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:32.451][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:32.453][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:32.455][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-28 16:02:32.457][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-28 16:02:32.459][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-28 16:02:32.461][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-28 16:02:32.463][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-28 16:02:32.465][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-28 16:02:32.466][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-28 16:02:32.468][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-28 16:02:32.470][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-28 16:02:32.472][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-28 16:02:32.473][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-28 16:02:32.475][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-28 16:02:32.477][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-28 16:02:32.479][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-28 16:02:32.481][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-28 16:02:32.482][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-28 16:02:32.484][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-28 16:02:32.486][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-28 16:02:32.488][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-28 16:02:32.490][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-28 16:02:32.492][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-28 16:02:32.494][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-28 16:02:32.495][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-28 16:02:32.497][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-28 16:02:32.499][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-28 16:02:32.501][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-28 16:02:32.502][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-28 16:02:32.504][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-28 16:02:32.506][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-28 16:02:32.508][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:32.510][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-28 16:02:32.511][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-28 16:02:32.513][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-28 16:02:32.515][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-28 16:02:32.517][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-28 16:02:32.518][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-28 16:02:32.520][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-28 16:02:32.522][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-28 16:02:32.524][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-28 16:02:32.525][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-28 16:02:32.527][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-28 16:02:32.529][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-28 16:02:32.531][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-28 16:02:32.532][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-28 16:02:32.534][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-28 16:02:32.536][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-28 16:02:32.542][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-28 16:02:32.544][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-28 16:02:32.546][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-28 16:02:32.548][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-28 16:02:32.550][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-28 16:02:32.552][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-28 16:02:32.556][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-28 16:02:32.559][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-28 16:02:32.562][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-28 16:02:32.565][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-28 16:02:32.568][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-28 16:02:32.571][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-28 16:02:32.574][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-28 16:02:32.578][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-28 16:02:32.582][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-28 16:02:32.585][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-28 16:02:32.588][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-28 16:02:32.590][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-28 16:02:32.593][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-28 16:02:32.596][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-28 16:02:32.600][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-28 16:02:32.603][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-28 16:02:32.606][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:32.609][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:32.610][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.614][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:32.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:32.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:32.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:32.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:32.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:32.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:32.758][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:32.764][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-28 16:02:32.767][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.768][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-28 16:02:32.769][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.771][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:32.772][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.773][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.774][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.776][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.777][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-28 16:02:32.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:32.780][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.781][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-28 16:02:32.782][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:32.783][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-28 16:02:32.783][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-28 16:02:32.785][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.786][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.787][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:32.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.791][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:32.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.794][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.796][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-28 16:02:32.796][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-28 16:02:32.797][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:32.798][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:32.799][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.801][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.802][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-28 16:02:32.805][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.806][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-28 16:02:32.807][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.809][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:32.810][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.811][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.813][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.817][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:32.819][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:32.821][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.823][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-28 16:02:32.826][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:32.829][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-28 16:02:32.829][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-28 16:02:32.829][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-28 16:02:32.829][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-28 16:02:32.829][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-28 16:02:32.829][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-28 16:02:32.833][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.836][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:32.839][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:32.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.845][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:32.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.853][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.856][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:32.856][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:32.860][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:32.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:32.865][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.867][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.871][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-28 16:02:32.875][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.878][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-28 16:02:32.881][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.883][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:32.886][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.888][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.892][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.897][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:32.900][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:32.905][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.908][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-28 16:02:32.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.912][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:32.915][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.919][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:32.919][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:32.919][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:32.921][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-28 16:02:32.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.928][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:32.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.937][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:32.937][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:32.937][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-28 16:02:32.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:32.941][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:32.943][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.946][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-28 16:02:32.949][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-28 16:02:32.953][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.956][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-28 16:02:32.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.960][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:32.962][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.964][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.967][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.969][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:32.972][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:32.975][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:32.977][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:32.979][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-28 16:02:32.982][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:32.984][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-28 16:02:32.984][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-28 16:02:32.986][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:32.988][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:32.991][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-28 16:02:32.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:32.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:32.996][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:32.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:33.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:33.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:33.006][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:33.006][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:33.006][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-28 16:02:33.008][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:33.010][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:33.012][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:33.015][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-28 16:02:33.018][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-28 16:02:33.021][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:33.025][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:33.029][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-28 16:02:33.033][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:33.036][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-28 16:02:33.053][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-28 16:02:33.062][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2026-02-28 16:02:33.080][biodb::testThat]
biodb.INFO [2026-02-28 16:02:33.083][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-28 16:02:33.085][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:33.087][biodb::testThat]
biodb.TRACE[2026-02-28 16:02:33.093][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2026-02-28 16:02:33.096][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-02-28 16:02:33.103][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-02-28 16:02:33.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-28 16:02:33.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:33.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:33.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:33.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:33.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:33.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-28 16:02:33.139][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.141][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.144][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.146][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.154][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.156][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.158][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.160][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.162][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.170][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.172][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.173][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.174][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.176][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.184][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.186][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.187][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.189][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.196][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.198][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.199][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.201][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.208][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.209][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.211][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.212][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.214][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.219][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-28 16:02:33.221][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.222][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.223][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.225][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-28 16:02:33.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.230][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:33.231][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:33.233][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.234][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.235][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:33.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:33.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.241][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:33.242][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:33.243][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.244][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:33.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:33.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.251][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:33.252][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:33.254][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.255][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.256][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:33.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:33.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.262][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:33.263][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:33.264][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.265][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.267][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:33.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:33.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.272][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-28 16:02:33.273][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.275][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.276][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-28 16:02:33.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.283][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.284][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.285][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.287][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.288][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.293][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.295][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.296][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.297][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.309][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-02-28 16:02:33.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.324][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-02-28 16:02:33.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.334][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.339][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-02-28 16:02:33.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.344][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.349][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.354][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-02-28 16:02:33.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.359][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.364][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.369][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-02-28 16:02:33.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.374][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.380][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:33.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:33.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.390][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.395][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:33.441][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2026-02-28 16:02:33.444][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:33.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:33.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.449][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:33.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:33.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.455][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:33.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:33.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:33.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:33.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.465][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:33.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:33.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:33.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:33.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:33.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:33.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.517][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.561][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.566][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:33.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.599][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.600][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.602][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.603][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:33.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:33.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.620][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-28 16:02:33.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.635][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-28 16:02:33.636][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.638][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.639][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.640][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-28 16:02:33.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:33.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-28 16:02:33.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.671][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-28 16:02:33.673][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.674][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.675][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-28 16:02:33.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:33.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.698][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:33.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:33.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.703][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:33.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:33.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:33.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:33.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.713][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:33.715][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:33.716][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.717][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:33.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:33.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.734][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:33.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:33.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.740][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:33.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:33.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.745][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:33.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:33.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.750][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:33.751][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:33.752][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.753][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.755][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:33.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:33.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.771][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.776][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.781][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.786][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.788][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.789][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.790][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:33.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.807][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.813][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.818][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.823][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.824][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.825][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.827][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.828][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:33.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.844][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.849][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.854][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.859][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.860][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.862][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.863][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.864][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:33.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.896][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.901][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.902][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.903][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.905][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:33.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.922][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.927][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.932][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.937][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.939][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.940][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.941][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.943][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:33.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.958][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.974][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.976][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.977][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.978][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.980][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:33.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:33.995][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:33.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:33.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.001][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.006][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.011][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.012][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.013][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.014][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:34.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:34.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:34.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:34.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.047][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:34.048][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:34.050][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.051][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:34.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:34.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.089][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.091][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.092][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.093][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:34.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:34.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:34.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:34.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:34.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:34.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.127][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:34.128][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:34.130][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.131][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:34.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:34.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.148][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.149][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.150][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.152][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.158][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.160][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.161][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.162][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.168][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.170][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.171][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.172][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.179][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.181][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.182][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.183][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.190][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.191][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.192][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.193][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.200][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.201][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.203][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.204][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.210][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:34.212][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:34.213][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.214][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.221][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:34.222][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:34.223][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.224][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.231][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.233][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.234][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.235][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.241][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:34.243][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:34.244][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.245][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.252][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.253][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.254][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.256][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.266][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.268][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.269][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.270][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.277][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:34.278][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:34.280][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.281][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.287][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.288][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.290][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.291][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.297][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.299][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.300][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.301][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.308][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2026-02-28 16:02:34.310][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-02-28 16:02:34.311][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-02-28 16:02:34.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-28 16:02:34.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:34.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:34.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:34.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:34.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:34.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-28 16:02:34.329][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.330][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.331][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.332][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.339][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.340][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.342][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.343][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.344][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.350][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.351][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.352][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.353][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.355][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.360][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.362][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.363][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.364][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.366][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.371][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.372][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.373][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.374][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.381][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.383][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.384][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.385][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.387][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.392][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-28 16:02:34.393][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.394][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.396][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.397][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-02-28 16:02:34.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.402][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:34.404][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:34.405][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.406][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:34.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:34.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.413][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:34.414][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:34.415][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.417][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:34.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:34.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.423][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.425][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.426][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.427][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.429][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:34.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.434][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:34.435][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:34.437][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.438][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.439][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:34.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:34.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.445][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-28 16:02:34.446][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.447][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.448][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-02-28 16:02:34.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.461][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.462][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.463][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.464][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.466][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.471][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.473][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.474][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.475][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.477][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.482][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-02-28 16:02:34.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:34.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.497][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-02-28 16:02:34.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.507][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:34.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.513][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-02-28 16:02:34.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:34.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.528][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-02-28 16:02:34.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.534][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:34.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.544][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-02-28 16:02:34.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.555][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:34.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:34.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:34.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.565][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.570][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.580][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:34.616][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2026-02-28 16:02:34.619][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:34.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:34.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.624][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:34.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:34.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.629][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:34.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:34.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.638][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:34.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:34.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.644][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:34.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:34.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:34.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:34.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.654][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:34.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:34.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.671][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.715][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.720][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.725][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:34.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.755][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.756][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.758][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.759][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:34.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:34.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.793][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.794][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.795][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.796][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:34.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.834][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.836][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.837][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.838][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:34.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:34.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:34.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:34.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:34.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.865][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:34.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:34.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.870][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:34.872][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:34.873][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.874][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:34.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:34.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.891][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:34.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:34.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.897][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:34.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:34.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.902][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:34.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:34.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.907][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:34.909][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:34.910][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.911][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.912][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:34.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:34.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.929][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.934][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.940][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.945][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.947][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.948][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.949][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.950][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:34.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.967][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.972][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.978][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.983][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.984][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.985][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.986][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:34.988][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:34.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:34.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.025][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.026][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.029][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:35.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:35.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:35.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:35.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:35.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:35.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.062][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:35.063][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:35.064][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.066][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:35.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.094][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.100][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.101][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.102][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.103][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.105][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.120][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.131][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.136][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.137][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.138][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.140][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.141][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.156][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.162][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.167][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.172][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.173][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.175][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.176][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.177][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.198][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.209][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.215][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.216][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.218][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.219][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.220][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.235][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.251][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.252][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.253][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.255][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:35.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:35.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.277][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:35.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:35.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:35.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:35.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.287][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:35.288][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:35.290][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.291][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:35.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:35.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.308][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:35.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:35.311][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.312][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.318][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.320][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-02-28 16:02:35.321][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.322][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.329][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.331][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-02-28 16:02:35.332][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.333][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.340][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.341][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-02-28 16:02:35.342][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.344][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.350][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.352][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:35.353][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.354][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.361][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.362][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:35.363][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.365][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.371][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:35.373][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:35.374][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.375][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.382][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:35.384][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:35.385][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.386][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.393][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.394][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:35.401][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.402][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.410][ef$get] Asked field names are: logp.
biodb.TRACE[2026-02-28 16:02:35.411][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-02-28 16:02:35.412][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.414][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.420][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:35.422][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:35.423][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.424][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.431][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:35.432][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:35.433][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.435][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.441][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:35.443][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:35.444][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.445][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.452][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:35.453][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-02-28 16:02:35.454][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.456][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:35.462][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:35.464][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-02-28 16:02:35.465][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.466][ef$get] fields variable is a list.
biodb.INFO [2026-02-28 16:02:35.476][biodb::testThat]
biodb.INFO [2026-02-28 16:02:35.478][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-28 16:02:35.479][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:35.480][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:35.483][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-28 16:02:35.487][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-28 16:02:35.490][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:35.491][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:35.492][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:35.494][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:35.495][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:35.496][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:35.555][biodb::testThat]
biodb.INFO [2026-02-28 16:02:35.556][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-28 16:02:35.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:35.559][biodb::testThat]
biodb.TRACE[2026-02-28 16:02:35.563][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:35.564][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:35.566][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:35.567][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:35.568][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2026-02-28 16:02:35.581][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-28 16:02:35.582][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:35.584][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:35.591][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:35.592][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:35.594][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:35.595][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:35.596][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:35.657][biodb::testThat]
biodb.INFO [2026-02-28 16:02:35.658][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-28 16:02:35.659][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:35.660][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:35.670][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-28 16:02:35.672][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:35.674][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:35.675][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:35.676][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:35.678][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:35.679][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:35.680][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:35.739][biodb::testThat]
biodb.INFO [2026-02-28 16:02:35.741][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-28 16:02:35.742][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:35.743][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:35.748][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-28 16:02:35.750][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:35.752][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:35.753][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:35.760][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:35.761][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:35.763][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:35.764][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:35.824][biodb::testThat]
biodb.INFO [2026-02-28 16:02:35.825][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-28 16:02:35.826][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:35.828][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:35.887][biodb::testThat]
biodb.INFO [2026-02-28 16:02:35.888][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-28 16:02:35.889][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:35.890][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:35.955][biodb::testThat]
biodb.INFO [2026-02-28 16:02:35.956][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:35.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:35.959][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:36.017][biodb::testThat]
biodb.INFO [2026-02-28 16:02:36.018][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:36.019][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:36.020][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-02-28 16:02:36.094][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:36.095][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:36.096][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:36.097][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:36.099][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:36.100][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:36.101][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:36.102][ef$get] fields variable is a list.
biodb.INFO [2026-02-28 16:02:36.104][biodb::testThat]
biodb.INFO [2026-02-28 16:02:36.106][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2026-02-28 16:02:36.107][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:36.108][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:36.118][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-02-28 16:02:36.119][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:36.121][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:36.122][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:36.124][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:36.125][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:36.126][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:36.127][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:36.186][biodb::testThat]
biodb.INFO [2026-02-28 16:02:36.188][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2026-02-28 16:02:36.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:36.190][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:36.194][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-28 16:02:36.195][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-28 16:02:36.197][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:36.198][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:36.200][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:36.201][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:36.202][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:36.203][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:36.268][biodb::testThat]
biodb.INFO [2026-02-28 16:02:36.269][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2026-02-28 16:02:36.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:36.272][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:36.275][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-28 16:02:36.277][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-28 16:02:36.279][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:36.280][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:36.281][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:36.282][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:36.284][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:36.285][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:36.344][biodb::testThat]
biodb.INFO [2026-02-28 16:02:36.346][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2026-02-28 16:02:36.347][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:36.348][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:36.352][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-28 16:02:36.354][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-28 16:02:36.355][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:36.357][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:36.358][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:36.359][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:36.361][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:36.362][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-02-28 16:02:36.425][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:36.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:36.428][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:36.429][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:36.430][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:36.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-28 16:02:36.433][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:36.434][ef$get] fields variable is a list.
biodb.INFO [2026-02-28 16:02:36.436][biodb::testThat]
biodb.INFO [2026-02-28 16:02:36.437][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2026-02-28 16:02:36.438][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:36.439][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:36.443][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-28 16:02:36.444][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-28 16:02:36.446][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:36.448][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:36.449][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:36.450][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:36.452][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:36.453][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:36.510][biodb::testThat]
biodb.INFO [2026-02-28 16:02:36.511][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2026-02-28 16:02:36.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:36.514][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:36.518][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-02-28 16:02:36.519][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-02-28 16:02:36.521][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:36.522][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:36.523][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:36.525][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:36.526][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:36.527][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-02-28 16:02:36.590][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-28 16:02:36.592][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2026-02-28 16:02:36.593][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-28 16:02:36.594][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:36.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:36.596][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:36.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:36.599][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-28 16:02:36.605][biodb::testContext]
biodb.INFO [2026-02-28 16:02:36.606][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:36.607][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2026-02-28 16:02:36.609][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:36.610][biodb::testContext]
biodb.INFO [2026-02-28 16:02:36.612][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:36.614][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:36.619][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:36.620][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-28 16:02:36.622][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-28 16:02:36.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.626][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-28 16:02:36.628][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-28 16:02:36.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.632][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-28 16:02:36.634][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-28 16:02:36.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.638][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-28 16:02:36.640][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-28 16:02:36.641][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-28 16:02:36.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.646][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-28 16:02:36.647][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-28 16:02:36.648][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-28 16:02:36.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.653][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-28 16:02:36.654][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-28 16:02:36.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.659][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-28 16:02:36.660][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-28 16:02:36.662][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-28 16:02:36.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.666][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-28 16:02:36.668][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-28 16:02:36.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.673][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-28 16:02:36.675][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-28 16:02:36.676][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-28 16:02:36.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.681][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:36.682][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-28 16:02:36.683][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-28 16:02:36.684][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-28 16:02:36.686][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-28 16:02:36.687][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-28 16:02:36.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.692][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-28 16:02:36.693][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-28 16:02:36.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.698][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-28 16:02:36.699][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-28 16:02:36.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.704][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-28 16:02:36.705][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-28 16:02:36.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.710][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-28 16:02:36.711][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-28 16:02:36.713][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-28 16:02:36.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.717][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:36.719][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-28 16:02:36.730][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-28 16:02:36.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.735][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-28 16:02:36.736][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-28 16:02:36.738][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-28 16:02:36.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.743][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-28 16:02:36.745][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.751][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-28 16:02:36.752][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.754][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:36.755][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.757][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.758][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.759][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.760][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:36.762][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:36.763][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.764][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-28 16:02:36.766][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:36.767][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.768][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.770][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:36.770][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:36.770][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:36.770][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:36.770][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:36.771][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:36.773][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:36.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:36.775][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:36.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:36.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:36.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.780][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:36.782][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:36.784][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.785][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.786][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-28 16:02:36.789][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.790][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:36.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:36.794][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.797][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.798][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.799][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:36.801][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:36.802][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.809][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-28 16:02:36.811][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:36.812][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.814][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.815][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:36.815][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:36.815][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:36.815][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:36.815][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:36.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:36.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:36.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:36.820][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:36.821][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:36.822][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:36.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.825][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.826][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:36.827][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:36.828][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.830][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.831][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-28 16:02:36.833][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.835][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-28 16:02:36.836][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.837][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:36.839][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.840][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.843][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.844][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:36.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:36.846][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.848][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-28 16:02:36.902][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:36.903][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.905][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.906][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.907][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:36.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:36.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:36.929][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:36.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:36.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:36.932][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.934][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:36.940][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:36.942][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.943][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.945][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-28 16:02:36.947][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.948][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:36.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.954][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:36.955][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.956][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.957][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.959][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.960][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:36.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:36.963][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.964][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-28 16:02:36.965][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:36.966][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.968][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:36.969][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:36.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:36.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:36.974][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:36.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:36.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:36.977][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:36.979][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:36.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:36.982][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:36.984][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:36.985][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:36.986][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:36.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:36.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:36.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.993][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[2026-02-28 16:02:36.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:36.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:36.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:36.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:36.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.073][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[2026-02-28 16:02:37.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.079][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[2026-02-28 16:02:37.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.086][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-28 16:02:37.088][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-28 16:02:37.089][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-28 16:02:37.091][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-28 16:02:37.093][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-28 16:02:37.095][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-28 16:02:37.097][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:37.098][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:37.100][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-28 16:02:37.102][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-28 16:02:37.104][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-28 16:02:37.105][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-28 16:02:37.107][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:37.109][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:37.111][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:37.113][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:37.114][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-28 16:02:37.116][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-28 16:02:37.118][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-28 16:02:37.120][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-28 16:02:37.122][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-28 16:02:37.123][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-28 16:02:37.125][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-28 16:02:37.127][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-28 16:02:37.129][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-28 16:02:37.131][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-28 16:02:37.132][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-28 16:02:37.134][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-28 16:02:37.136][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-28 16:02:37.138][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-28 16:02:37.140][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-28 16:02:37.142][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-28 16:02:37.143][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-28 16:02:37.145][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-28 16:02:37.147][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-28 16:02:37.149][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-28 16:02:37.150][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-28 16:02:37.152][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-28 16:02:37.154][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-28 16:02:37.156][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-28 16:02:37.157][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-28 16:02:37.159][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-28 16:02:37.161][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-28 16:02:37.163][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-28 16:02:37.164][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-28 16:02:37.166][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:37.168][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-28 16:02:37.170][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-28 16:02:37.172][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-28 16:02:37.173][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-28 16:02:37.180][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-28 16:02:37.182][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-28 16:02:37.184][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-28 16:02:37.186][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-28 16:02:37.187][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-28 16:02:37.189][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-28 16:02:37.191][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-28 16:02:37.193][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-28 16:02:37.194][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-28 16:02:37.196][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-28 16:02:37.198][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-28 16:02:37.199][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-28 16:02:37.201][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-28 16:02:37.203][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-28 16:02:37.205][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-28 16:02:37.207][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-28 16:02:37.209][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-28 16:02:37.211][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-28 16:02:37.212][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-28 16:02:37.214][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-28 16:02:37.216][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-28 16:02:37.218][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-28 16:02:37.219][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-28 16:02:37.221][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-28 16:02:37.223][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-28 16:02:37.224][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-28 16:02:37.226][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-28 16:02:37.228][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-28 16:02:37.230][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-28 16:02:37.231][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-28 16:02:37.233][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-28 16:02:37.235][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-28 16:02:37.237][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-28 16:02:37.238][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-28 16:02:37.240][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:37.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:37.243][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.245][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.262][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[2026-02-28 16:02:37.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.270][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[2026-02-28 16:02:37.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:37.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:37.383][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:37.385][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-02-28 16:02:37.387][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.388][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-02-28 16:02:37.390][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:37.392][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.393][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.394][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.396][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.397][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-02-28 16:02:37.398][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:37.399][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.401][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-02-28 16:02:37.402][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:37.403][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-02-28 16:02:37.403][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-02-28 16:02:37.405][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:37.406][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:37.407][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:37.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:37.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:37.411][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:37.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:37.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:37.414][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.415][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-02-28 16:02:37.415][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-02-28 16:02:37.417][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:37.418][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:37.419][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.420][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:37.422][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-02-28 16:02:37.424][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.426][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-02-28 16:02:37.427][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.428][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:37.429][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.431][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.432][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.433][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.434][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:37.436][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:37.437][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.438][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-02-28 16:02:37.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:37.441][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-02-28 16:02:37.441][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-02-28 16:02:37.441][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-02-28 16:02:37.441][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-02-28 16:02:37.441][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-02-28 16:02:37.441][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-02-28 16:02:37.442][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:37.443][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:37.444][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:37.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:37.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:37.448][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:37.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:37.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:37.451][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.453][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:37.453][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:37.454][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:37.455][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:37.456][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.458][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:37.459][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-02-28 16:02:37.462][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:37.463][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-02-28 16:02:37.464][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.465][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:37.466][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.468][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.469][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.470][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.471][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:37.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:37.474][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.475][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-02-28 16:02:37.476][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.478][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-02-28 16:02:37.479][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:37.481][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:37.481][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:37.481][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:37.482][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-28 16:02:37.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:37.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:37.485][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:37.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:37.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:37.489][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.490][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:37.490][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:37.490][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-28 16:02:37.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:37.493][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:37.494][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.495][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-28 16:02:37.497][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-28 16:02:37.499][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.500][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-02-28 16:02:37.502][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:37.504][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.505][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.507][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.508][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.509][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:37.510][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:37.512][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.513][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-02-28 16:02:37.514][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:37.516][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-02-28 16:02:37.516][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-02-28 16:02:37.522][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:37.523][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:37.525][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-02-28 16:02:37.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:37.527][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:37.529][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:37.530][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:37.531][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:37.532][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:37.534][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:37.534][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-02-28 16:02:37.534][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-02-28 16:02:37.535][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:37.536][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:37.537][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:37.539][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-02-28 16:02:37.540][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-02-28 16:02:37.542][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:37.544][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:37.546][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-02-28 16:02:37.548][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:37.550][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-02-28 16:02:37.556][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2026-02-28 16:02:37.561][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2026-02-28 16:02:37.567][biodb::testThat]
biodb.INFO [2026-02-28 16:02:37.568][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-28 16:02:37.569][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:37.570][biodb::testThat]
biodb.TRACE[2026-02-28 16:02:37.574][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2026-02-28 16:02:37.575][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2026-02-28 16:02:37.579][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2026-02-28 16:02:37.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-28 16:02:37.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:37.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:37.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:37.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:37.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:37.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-28 16:02:37.596][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.598][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.599][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.600][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.607][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.608][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.609][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.611][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.613][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.618][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.624][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.634][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:37.669][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2026-02-28 16:02:37.671][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:37.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:37.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.676][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-02-28 16:02:37.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-02-28 16:02:37.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.681][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:37.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-02-28 16:02:37.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:37.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:37.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.691][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:37.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:37.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.696][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:37.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:37.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.707][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:37.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:37.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.724][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.767][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.777][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-02-28 16:02:37.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.806][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.807][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.808][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.810][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.827][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.832][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.837][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.842][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.844][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.845][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.846][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.847][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.864][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:37.865][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:37.866][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.868][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:37.874][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.876][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:37.877][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:37.883][ef$get] fields variable is a list.
biodb.INFO [2026-02-28 16:02:37.895][biodb::testThat]
biodb.INFO [2026-02-28 16:02:37.896][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-28 16:02:37.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:37.898][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:37.901][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-02-28 16:02:37.906][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:37.908][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:37.909][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:37.911][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:37.912][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:37.913][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:37.915][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-28 16:02:37.973][biodb::testThat]
biodb.INFO [2026-02-28 16:02:37.975][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-28 16:02:37.976][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:37.977][biodb::testThat]
biodb.INFO [2026-02-28 16:02:37.986][biodb::testThat]
biodb.INFO [2026-02-28 16:02:37.987][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-28 16:02:37.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:37.989][biodb::testThat]
biodb.WARN [2026-02-28 16:02:37.993][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-28 16:02:37.997][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-28 16:02:38.008][biodb::testThat]
biodb.INFO [2026-02-28 16:02:38.010][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-28 16:02:38.011][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:38.012][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:38.017][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-02-28 16:02:38.019][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-02-28 16:02:38.021][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-02-28 16:02:38.022][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-02-28 16:02:38.024][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-02-28 16:02:38.025][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-02-28 16:02:38.026][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-02-28 16:02:38.028][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-28 16:02:38.096][biodb::testThat]
biodb.INFO [2026-02-28 16:02:38.098][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-28 16:02:38.099][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:38.100][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-28 16:02:38.162][biodb::testThat]
biodb.INFO [2026-02-28 16:02:38.163][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-28 16:02:38.164][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:38.165][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-28 16:02:38.229][biodb::testThat]
biodb.INFO [2026-02-28 16:02:38.230][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:38.232][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:38.233][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-28 16:02:38.291][biodb::testThat]
biodb.INFO [2026-02-28 16:02:38.292][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:38.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:38.294][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-02-28 16:02:38.353][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-28 16:02:38.354][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2026-02-28 16:02:38.355][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-28 16:02:38.356][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:38.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:38.359][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:38.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:38.366][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:38.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]

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

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

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

'R CMD check' output

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


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

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

Installation output

biodbNcbi.Rcheck/00install.out

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