Back to Long Tests report for BioC 3.22

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

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

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-02-07 09:55 -0500 (Sat, 07 Feb 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -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 biodbHmdb on merida1

To the developers/maintainers of the biodbHmdb 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: biodbHmdb
Version: 1.16.0
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 biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-02-07 16:01:18 -0500 (Sat, 07 Feb 2026)
EndedAt: 2026-02-07 16:02:53 -0500 (Sat, 07 Feb 2026)
EllapsedTime: 95.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2026-02-07 16:02:48.845][biodb::testContext]
biodb.INFO [2026-02-07 16:02:48.849][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:48.850][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-07 16:02:48.851][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:48.852][biodb::testContext]
biodb.INFO [2026-02-07 16:02:48.859][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:48.861][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:48.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:48.870][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-07 16:02:48.871][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-07 16:02:48.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.876][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-07 16:02:48.899][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-07 16:02:48.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.904][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-07 16:02:48.906][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-07 16:02:48.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.910][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-07 16:02:48.911][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-07 16:02:48.913][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-07 16:02:48.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.916][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[2026-02-07 16:02:48.917][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-07 16:02:48.919][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-07 16:02:48.920][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-07 16:02:48.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.925][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-07 16:02:48.926][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-07 16:02:48.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.930][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-07 16:02:48.932][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-07 16:02:48.933][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-07 16:02:48.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.938][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-07 16:02:48.939][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-07 16:02:48.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.944][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-07 16:02:48.945][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-07 16:02:48.946][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-07 16:02:48.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.951][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:48.952][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-07 16:02:48.953][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-07 16:02:48.955][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-07 16:02:48.956][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-07 16:02:48.957][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-07 16:02:48.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.962][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-07 16:02:48.963][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-07 16:02:48.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.968][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-07 16:02:48.969][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-07 16:02:48.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.974][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-07 16:02:48.975][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-07 16:02:48.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.980][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-07 16:02:48.981][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-07 16:02:48.982][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-07 16:02:48.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:48.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:48.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:48.987][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:48.988][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-07 16:02:48.999][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-07 16:02:49.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.003][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-07 16:02:49.005][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-07 16:02:49.006][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-07 16:02:49.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.010][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[2026-02-07 16:02:49.013][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-07 16:02:49.055][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.082][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-07 16:02:49.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.085][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:49.086][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.087][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.089][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.090][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.091][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:49.092][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:49.094][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.095][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-07 16:02:49.096][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:49.097][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.098][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.100][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:49.100][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:49.100][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:49.100][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:49.100][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:49.101][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:49.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:49.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.108][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.109][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:49.112][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:49.113][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.114][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.115][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-07 16:02:49.118][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.119][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:49.120][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.121][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:49.122][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.124][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.125][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.126][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.127][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:49.129][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:49.130][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.131][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-07 16:02:49.133][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:49.134][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.135][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.136][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:49.136][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:49.136][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:49.136][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:49.136][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:49.138][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:49.139][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.141][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:49.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.145][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.146][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.147][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:49.148][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:49.150][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.151][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.152][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-07 16:02:49.155][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.156][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-07 16:02:49.157][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.158][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:49.160][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.161][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.162][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.163][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.165][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:49.166][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:49.167][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.168][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-07 16:02:49.170][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:49.171][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.172][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.173][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.175][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:49.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.178][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:49.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.183][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.184][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:49.185][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:49.187][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.188][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.189][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-07 16:02:49.192][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.193][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:49.194][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.195][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:49.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.198][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.199][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.202][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:49.203][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:49.204][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.205][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-07 16:02:49.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:49.208][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.209][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.210][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.212][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:49.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.215][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:49.216][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.219][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.220][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.221][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:49.222][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:49.223][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.225][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.229][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:49.230][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.251][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[2026-02-07 16:02:49.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.259][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[2026-02-07 16:02:49.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.270][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[2026-02-07 16:02:49.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.332][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[2026-02-07 16:02:49.333][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-07 16:02:49.338][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-07 16:02:49.339][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-07 16:02:49.341][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-07 16:02:49.343][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-07 16:02:49.344][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-07 16:02:49.346][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:49.348][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:49.349][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-07 16:02:49.351][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-07 16:02:49.353][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-07 16:02:49.354][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-07 16:02:49.356][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:49.358][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:49.359][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:49.361][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:49.363][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-07 16:02:49.364][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-07 16:02:49.366][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-07 16:02:49.368][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-07 16:02:49.370][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-07 16:02:49.372][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-07 16:02:49.373][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-07 16:02:49.375][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-07 16:02:49.377][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-07 16:02:49.379][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-07 16:02:49.380][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-07 16:02:49.382][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-07 16:02:49.384][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-07 16:02:49.386][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-07 16:02:49.387][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-07 16:02:49.389][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-07 16:02:49.391][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-07 16:02:49.393][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-07 16:02:49.394][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-07 16:02:49.396][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-07 16:02:49.398][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-07 16:02:49.400][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-07 16:02:49.401][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-07 16:02:49.403][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-07 16:02:49.405][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-07 16:02:49.407][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-07 16:02:49.408][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-07 16:02:49.410][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-07 16:02:49.412][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-07 16:02:49.413][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:49.415][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-07 16:02:49.417][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-07 16:02:49.418][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-07 16:02:49.420][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-07 16:02:49.422][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-07 16:02:49.423][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-07 16:02:49.425][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-07 16:02:49.427][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-07 16:02:49.428][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-07 16:02:49.430][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-07 16:02:49.432][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-07 16:02:49.434][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-07 16:02:49.435][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-07 16:02:49.437][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-07 16:02:49.439][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-07 16:02:49.440][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-07 16:02:49.442][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-07 16:02:49.444][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-07 16:02:49.446][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-07 16:02:49.447][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-07 16:02:49.449][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-07 16:02:49.451][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-07 16:02:49.452][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-07 16:02:49.454][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-07 16:02:49.456][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-07 16:02:49.458][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-07 16:02:49.459][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-07 16:02:49.461][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-07 16:02:49.463][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-07 16:02:49.464][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-07 16:02:49.466][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-07 16:02:49.468][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-07 16:02:49.470][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-07 16:02:49.471][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-07 16:02:49.473][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-07 16:02:49.475][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-07 16:02:49.476][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-07 16:02:49.484][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-07 16:02:49.486][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:49.489][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:49.491][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.493][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.523][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[2026-02-07 16:02:49.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.572][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[2026-02-07 16:02:49.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.585][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[2026-02-07 16:02:49.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.600][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.DEBUG[2026-02-07 16:02:49.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.631][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.WARN [2026-02-07 16:02:49.632][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-02-07 16:02:49.642][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-02-07 16:02:49.660][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-02-07 16:02:49.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:49.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:49.670][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:49.683][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-02-07 16:02:49.685][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.686][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.689][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:49.690][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.691][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-02-07 16:02:49.693][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.694][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.695][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-07 16:02:49.696][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:49.698][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.699][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-02-07 16:02:49.700][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-02-07 16:02:49.701][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-02-07 16:02:49.703][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:49.704][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:49.704][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-02-07 16:02:49.704][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-02-07 16:02:49.705][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:49.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:49.710][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:49.711][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:49.712][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:49.714][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-02-07 16:02:49.714][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-02-07 16:02:49.715][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:49.716][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:49.717][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:49.718][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:49.726][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-02-07 16:02:49.728][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-07 16:02:49.730][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-07 16:02:49.732][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-07 16:02:49.734][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:49.756][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-02-07 16:02:49.772][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-02-07 16:02:49.781][biodb::testThat]
biodb.INFO [2026-02-07 16:02:49.783][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-07 16:02:49.784][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:49.785][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:49.790][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-02-07 16:02:49.792][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:49.796][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-02-07 16:02:49.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:49.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:49.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:49.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:49.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:49.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:49.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:49.839][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:49.840][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:49.842][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.843][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:49.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:49.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.876][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:49.877][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:49.879][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.880][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.915][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:49.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:49.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.921][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:49.922][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:49.923][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.924][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.926][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:49.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:49.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.931][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:49.932][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:49.934][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.935][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.936][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:49.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:49.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.941][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:49.943][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:49.944][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.945][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:49.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:49.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.952][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:49.953][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:49.954][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.955][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:49.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:49.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.962][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:49.963][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:49.964][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.965][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.967][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:49.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:49.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.972][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:49.973][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:49.974][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.976][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:49.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:49.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.982][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:49.983][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:49.985][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.986][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.987][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:49.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:49.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.992][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:49.994][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:49.995][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:49.996][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:49.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:49.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:50.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.002][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.004][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.005][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.006][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.008][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.013][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:50.014][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:50.015][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.016][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:50.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:50.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.023][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.024][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.025][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.027][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.033][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.034][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.036][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.037][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.043][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.046][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.047][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.053][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.055][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.056][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.057][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.059][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.068][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:50.069][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:50.070][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.071][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.073][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:50.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.078][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-02-07 16:02:50.079][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:50.080][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.082][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.083][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-02-07 16:02:50.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:50.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.147][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.152][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.157][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.162][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:50.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:50.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.167][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:50.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:50.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.172][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:50.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:50.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.206][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:50.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:50.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.211][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:50.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:50.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.216][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:50.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:50.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.221][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:50.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:50.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:50.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:50.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.231][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:50.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:50.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.236][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:50.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:50.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:50.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:50.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:50.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:50.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.251][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.256][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.261][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.266][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:50.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:50.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:50.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:50.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:50.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:50.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.314][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.319][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.324][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:50.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.358][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.363][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.368][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.373][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.378][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.383][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.387][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:50.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:50.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.392][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:50.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:50.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.397][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:50.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:50.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.402][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-07 16:02:50.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-07 16:02:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:50.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.507][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.513][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.522][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:50.557][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-02-07 16:02:50.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:50.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:50.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:50.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:50.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.570][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:50.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:50.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:50.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:50.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.592][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.636][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.641][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.646][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-07 16:02:50.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.675][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.676][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.678][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.679][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:50.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:50.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.696][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.701][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.706][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.711][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.712][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.713][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.715][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:50.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.751][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.752][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.754][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.755][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:50.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.771][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.777][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.781][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.786][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.788][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.789][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.790][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.791][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:50.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.822][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.823][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.824][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.826][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:50.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.842][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.847][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.852][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.857][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.859][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.860][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.861][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:50.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.893][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.895][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.897][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:50.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:50.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.913][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.918][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.923][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.928][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.930][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.931][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.932][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.933][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:50.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:50.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.963][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.968][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.969][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.970][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.972][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.973][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:50.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:50.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.988][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.993][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:50.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:50.998][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:50.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:51.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.003][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:51.004][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:51.006][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.007][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.008][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:51.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:51.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.038][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.040][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.041][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.042][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.064][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.069][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.074][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.075][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.076][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.077][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.079][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.094][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.099][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.104][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.109][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.110][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.111][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.113][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.114][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.129][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.135][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.140][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.145][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.146][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.147][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.149][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.150][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.166][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:51.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:51.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.176][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:51.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:51.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:51.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:51.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.186][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:51.187][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:51.188][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.189][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.191][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:51.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:51.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:51.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:51.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:51.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:51.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:51.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:51.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.222][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:51.224][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:51.225][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.226][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:51.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:51.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.260][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.261][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.263][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.264][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.281][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.287][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.292][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.297][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.299][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.300][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.301][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.302][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.317][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:51.319][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:51.320][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.321][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.327][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-07 16:02:51.329][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-07 16:02:51.330][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.331][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.337][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.339][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:51.340][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.341][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.347][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-07 16:02:51.348][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-07 16:02:51.350][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.351][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.357][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:51.358][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-07 16:02:51.360][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.361][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.367][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.368][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-07 16:02:51.369][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.370][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.376][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.378][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-07 16:02:51.379][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.380][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.386][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.388][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-07 16:02:51.389][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.390][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.401][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:51.402][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:51.403][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.404][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.411][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:51.412][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:51.413][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.415][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.421][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:51.422][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:51.423][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.424][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.432][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:51.433][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.434][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.440][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:51.442][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-07 16:02:51.443][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.444][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.450][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.451][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-07 16:02:51.453][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.454][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.460][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:51.461][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:51.462][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.464][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.470][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:51.471][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-07 16:02:51.472][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.473][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.480][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:51.481][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:51.482][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.483][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:51.490][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-07 16:02:51.491][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-07 16:02:51.492][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.493][ef$get] fields variable is a list.
biodb.INFO [2026-02-07 16:02:51.503][biodb::testThat]
biodb.INFO [2026-02-07 16:02:51.505][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-07 16:02:51.506][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:51.507][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:51.525][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-07 16:02:51.530][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-07 16:02:51.532][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-07 16:02:51.571][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-07 16:02:51.573][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-07 16:02:51.574][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-07 16:02:51.748][biodb::testThat]
biodb.INFO [2026-02-07 16:02:51.749][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-07 16:02:51.750][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:51.752][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:51.756][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:51.757][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:51.758][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:51.759][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:51.761][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-02-07 16:02:51.791][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-07 16:02:51.859][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-07 16:02:51.861][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-07 16:02:51.863][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-07 16:02:51.864][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-07 16:02:51.881][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-07 16:02:51.952][biodb::testThat]
biodb.INFO [2026-02-07 16:02:51.953][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-07 16:02:51.954][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:51.956][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:51.965][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-07 16:02:51.967][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-07 16:02:51.969][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-07 16:02:51.970][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-07 16:02:51.972][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-07 16:02:51.973][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-07 16:02:52.034][biodb::testThat]
biodb.INFO [2026-02-07 16:02:52.035][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-07 16:02:52.037][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:52.038][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:52.043][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-07 16:02:52.044][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-07 16:02:52.046][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-07 16:02:52.048][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-07 16:02:52.049][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-07 16:02:52.050][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-07 16:02:52.106][biodb::testThat]
biodb.INFO [2026-02-07 16:02:52.108][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-07 16:02:52.109][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:52.110][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-07 16:02:52.172][biodb::testThat]
biodb.INFO [2026-02-07 16:02:52.174][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-07 16:02:52.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:52.176][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-07 16:02:52.234][biodb::testThat]
biodb.INFO [2026-02-07 16:02:52.236][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:52.237][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:52.238][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-07 16:02:52.297][biodb::testThat]
biodb.INFO [2026-02-07 16:02:52.298][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:52.299][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:52.300][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-02-07 16:02:52.379][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:52.380][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:52.382][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:52.383][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:52.384][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:52.385][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:52.386][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:52.388][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:52.389][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:52.390][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:52.391][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:52.393][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:52.394][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:52.395][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:52.396][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:52.398][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:52.399][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-07 16:02:52.400][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-07 16:02:52.401][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:52.403][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:52.404][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:52.405][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-07 16:02:52.406][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:52.407][ef$get] fields variable is a list.
biodb.INFO [2026-02-07 16:02:52.409][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-07 16:02:52.410][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-02-07 16:02:52.411][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-07 16:02:52.412][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:52.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:52.415][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:52.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:52.417][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:52.418][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".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, 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$download()
 8.             └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$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$getEntryContent(ids)
 7.           └─self$download()
 8.             └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─private$bdb$getFactory()$getEntry(...)
 6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 7.           └─conn$getEntryContent(ids)
 8.             └─self$download()
 9.               └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can get a URL pointing to the entry page. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): We can get a URL pointing to the entry image. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): The entry page URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)

[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
Error:
! Test failures.
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 biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.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 ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* 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 ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)