Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-20 23:55 -0500 (Sat, 20 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
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: 2025-12-20 09:55 -0500 (Sat, 20 Dec 2025)
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: 2025-12-20 16:01:19 -0500 (Sat, 20 Dec 2025)
EndedAt: 2025-12-20 16:02:48 -0500 (Sat, 20 Dec 2025)
EllapsedTime: 89.4 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"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(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 [2025-12-20 16:02:43.861][biodb::testContext]
biodb.INFO [2025-12-20 16:02:43.865][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:43.866][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-20 16:02:43.868][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:43.869][biodb::testContext]
biodb.INFO [2025-12-20 16:02:43.876][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:43.878][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:43.886][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:43.888][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-20 16:02:43.889][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-20 16:02:43.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.894][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-20 16:02:43.920][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-20 16:02:43.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.925][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-20 16:02:43.926][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-20 16:02:43.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.941][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-20 16:02:43.942][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-20 16:02:43.943][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-20 16:02:43.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.948][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-20 16:02:43.949][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-20 16:02:43.950][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-20 16:02:43.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.955][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-20 16:02:43.956][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-20 16:02:43.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.961][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-20 16:02:43.962][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-20 16:02:43.963][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-20 16:02:43.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.968][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-20 16:02:43.969][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-20 16:02:43.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.972][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[2025-12-20 16:02:43.974][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-20 16:02:43.975][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-20 16:02:43.977][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-20 16:02:43.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.981][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:43.982][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-20 16:02:43.984][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-20 16:02:43.985][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-20 16:02:43.986][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-20 16:02:43.988][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-20 16:02:43.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.992][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-20 16:02:43.994][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-20 16:02:43.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:43.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:43.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:43.998][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-20 16:02:44.000][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-20 16:02:44.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.004][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-20 16:02:44.006][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-20 16:02:44.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.010][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-20 16:02:44.011][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-20 16:02:44.013][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-20 16:02:44.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.017][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:44.019][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-20 16:02:44.029][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-20 16:02:44.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.034][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-20 16:02:44.035][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-20 16:02:44.037][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-20 16:02:44.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.044][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-20 16:02:44.087][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.109][self$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[2025-12-20 16:02:44.110][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.112][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:44.113][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.114][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.115][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.117][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.118][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:44.119][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:44.120][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.122][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-20 16:02:44.123][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:44.124][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.125][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.127][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:44.127][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:44.127][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:44.127][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:44.127][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:44.128][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:44.129][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.132][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:44.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.135][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.137][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.138][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:44.139][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:44.140][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.142][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.143][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-20 16:02:44.145][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.147][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:44.148][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.149][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:44.151][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.152][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.153][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.154][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.156][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:44.157][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:44.163][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.164][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-20 16:02:44.166][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:44.167][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.168][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.169][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:44.169][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:44.169][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:44.169][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:44.169][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:44.171][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:44.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.174][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:44.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.178][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.179][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.180][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:44.182][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:44.183][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.184][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.186][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-20 16:02:44.188][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.189][self$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[2025-12-20 16:02:44.190][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.192][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:44.193][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.194][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.196][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.197][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.198][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:44.199][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:44.201][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.202][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-20 16:02:44.203][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:44.204][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.206][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.207][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.208][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:44.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:44.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.217][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:44.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:44.220][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.222][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.223][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-20 16:02:44.225][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.227][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:44.228][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.230][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:44.231][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.233][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.234][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.235][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.237][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:44.238][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:44.239][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.241][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-20 16:02:44.242][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:44.243][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.245][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.246][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.248][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:44.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.252][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:44.253][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.256][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.258][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.259][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:44.261][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:44.262][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.264][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.268][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:44.270][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.366][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-20 16:02:44.371][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-20 16:02:44.373][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-20 16:02:44.375][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-20 16:02:44.378][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-20 16:02:44.380][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:02:44.382][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:44.389][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:44.391][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-20 16:02:44.393][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:02:44.394][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:02:44.396][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-20 16:02:44.398][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:44.400][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:44.402][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:44.404][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:44.405][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-20 16:02:44.407][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-20 16:02:44.409][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-20 16:02:44.411][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-20 16:02:44.412][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-20 16:02:44.414][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-20 16:02:44.416][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-20 16:02:44.417][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-20 16:02:44.419][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-20 16:02:44.421][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-20 16:02:44.423][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-20 16:02:44.424][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-20 16:02:44.426][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-20 16:02:44.428][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-20 16:02:44.429][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-20 16:02:44.431][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-20 16:02:44.433][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-20 16:02:44.435][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-20 16:02:44.436][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-20 16:02:44.438][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-20 16:02:44.440][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-20 16:02:44.441][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-20 16:02:44.443][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-20 16:02:44.445][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-20 16:02:44.446][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-20 16:02:44.448][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-20 16:02:44.450][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-20 16:02:44.452][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-20 16:02:44.453][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-20 16:02:44.455][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:44.457][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-20 16:02:44.458][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-20 16:02:44.460][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-20 16:02:44.462][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-20 16:02:44.464][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-20 16:02:44.465][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-20 16:02:44.467][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-20 16:02:44.469][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-20 16:02:44.470][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-20 16:02:44.472][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-20 16:02:44.474][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-20 16:02:44.476][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-20 16:02:44.477][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-20 16:02:44.479][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-20 16:02:44.481][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-20 16:02:44.482][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-20 16:02:44.484][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-20 16:02:44.486][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-20 16:02:44.488][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-20 16:02:44.489][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-20 16:02:44.491][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-20 16:02:44.493][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-20 16:02:44.495][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-20 16:02:44.497][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-20 16:02:44.498][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-20 16:02:44.500][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-20 16:02:44.502][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-20 16:02:44.503][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-20 16:02:44.505][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-20 16:02:44.507][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-20 16:02:44.509][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-20 16:02:44.510][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-20 16:02:44.512][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-20 16:02:44.514][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-20 16:02:44.515][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-20 16:02:44.517][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-20 16:02:44.519][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-20 16:02:44.526][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-20 16:02:44.528][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:44.531][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:44.532][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.535][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-12-20 16:02:44.678][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-12-20 16:02:44.688][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-12-20 16:02:44.706][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-12-20 16:02:44.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:44.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:44.717][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:44.730][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-12-20 16:02:44.733][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.735][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.739][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:44.741][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.742][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-12-20 16:02:44.744][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.746][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.747][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:44.749][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:44.751][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.752][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-12-20 16:02:44.754][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-12-20 16:02:44.755][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-12-20 16:02:44.758][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:44.759][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:44.759][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-12-20 16:02:44.759][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-12-20 16:02:44.761][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:44.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:44.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:44.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:44.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:44.770][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-12-20 16:02:44.770][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-12-20 16:02:44.771][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:44.772][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:44.774][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:44.775][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:44.784][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-12-20 16:02:44.786][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:02:44.788][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:02:44.790][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:02:44.792][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:44.820][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-12-20 16:02:44.837][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-12-20 16:02:44.846][biodb::testThat]
biodb.INFO [2025-12-20 16:02:44.848][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-20 16:02:44.849][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:44.850][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:44.855][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[2025-12-20 16:02:44.857][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:02:44.861][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-12-20 16:02:44.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:02:44.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:44.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:44.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:44.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:44.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:44.894][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:44.906][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:44.907][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:44.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:44.911][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:44.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:44.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:44.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:44.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:44.935][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:44.936][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:44.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:44.939][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:44.975][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:44.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:44.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:44.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:44.980][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:44.982][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:44.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:44.984][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:44.986][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:44.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:44.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:44.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:44.991][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:44.993][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:44.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:44.995][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:44.997][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:44.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:44.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.002][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.003][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.006][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.013][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.014][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.017][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.033][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.035][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.037][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.039][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.044][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.045][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.048][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.049][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.055][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.056][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.058][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.060][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.065][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.067][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.069][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.071][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.076][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:45.078][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:45.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.080][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.082][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:45.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:45.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.088][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:45.089][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:45.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.092][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:45.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.102][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.105][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.113][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.116][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.119][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.128][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.131][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.134][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.143][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:45.145][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:45.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.149][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.151][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:45.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:45.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.161][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:45.162][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:45.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.166][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.168][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:45.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:45.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.176][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-12-20 16:02:45.179][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:45.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.183][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.185][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-12-20 16:02:45.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:45.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.303][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:45.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:45.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.308][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:45.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:45.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.314][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:45.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:45.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.319][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:45.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:45.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.324][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:45.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:45.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.329][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:45.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:45.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:45.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.365][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.370][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:45.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.381][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.386][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:45.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:45.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:45.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.402][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:45.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:45.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.407][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:45.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:45.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.413][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:45.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:45.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.418][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:45.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:45.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.424][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:45.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:45.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.429][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:45.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:45.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.434][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:45.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:45.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:45.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:45.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:45.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:45.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:45.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:45.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:45.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:45.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.481][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.486][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.491][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:45.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:45.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.528][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.533][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.538][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:45.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.543][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.548][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.553][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.558][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:45.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:45.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.563][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:45.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:45.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:45.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:45.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.573][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-20 16:02:45.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.593][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-20 16:02:45.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:45.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:45.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:45.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.651][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.656][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.666][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:45.715][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-12-20 16:02:45.720][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:45.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:45.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.727][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:45.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:45.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.734][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:45.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:45.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.740][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:45.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:45.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.758][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.831][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.839][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.846][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:45.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.877][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.879][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.881][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:45.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:45.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.904][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.911][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.918][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.926][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.929][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.932][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.933][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:45.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.973][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.975][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.979][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:45.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:45.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:45.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.008][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.017][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.026][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.035][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.038][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.042][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.044][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.082][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.083][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.085][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.102][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.107][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.112][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.117][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.118][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.121][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.122][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:46.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:46.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:46.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:46.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:46.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:46.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.152][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:46.153][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:46.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.156][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:46.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:46.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.172][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:46.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:46.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.177][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:46.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:46.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.182][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:46.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:46.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.187][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:46.188][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:46.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.191][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.192][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:46.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:46.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.207][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:46.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:46.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.212][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:46.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:46.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:46.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:46.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.226][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:46.228][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:46.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.230][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:46.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:46.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.246][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.251][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.256][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.261][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.262][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.265][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.266][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.297][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.298][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.300][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.317][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.332][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.334][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.336][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.338][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.353][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.359][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.364][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.369][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.370][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.373][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.374][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.399][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.409][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.410][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.413][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.429][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:46.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:46.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.435][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:46.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:46.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.440][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:46.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:46.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.445][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:46.446][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:46.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.449][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.450][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:46.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:46.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:46.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:46.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:46.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:46.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:46.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:46.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.481][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:46.482][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:46.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.485][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:46.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:46.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.516][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.517][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.519][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.537][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.542][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.547][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.557][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.558][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.561][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.562][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.579][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:46.580][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:46.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.583][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.590][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.592][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:46.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.594][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.601][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.602][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:46.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.605][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.612][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.613][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:46.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.616][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.622][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:46.624][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:46.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.626][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.633][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.635][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:46.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.638][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.648][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.651][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:46.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.654][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.662][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.663][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:46.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.666][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.672][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:46.673][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:46.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.675][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.682][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:46.683][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:46.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.686][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.693][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:46.695][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:46.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.699][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.707][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.709][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:46.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.713][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.724][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.727][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:46.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.730][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.737][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.739][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:46.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.743][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.749][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:46.751][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:46.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.754][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.760][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.766][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:46.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.769][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.775][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:46.777][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:46.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.779][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:46.786][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:46.788][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:46.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:46.793][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:46.805][biodb::testThat]
biodb.INFO [2025-12-20 16:02:46.806][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-20 16:02:46.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:46.808][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:46.827][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-20 16:02:46.830][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:02:46.833][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-20 16:02:46.873][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-20 16:02:46.875][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-20 16:02:46.876][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:47.052][biodb::testThat]
biodb.INFO [2025-12-20 16:02:47.053][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-20 16:02:47.055][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:47.056][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:47.060][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:47.061][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:47.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:47.064][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:47.071][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-12-20 16:02:47.100][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-20 16:02:47.163][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:02:47.165][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-20 16:02:47.166][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-20 16:02:47.168][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-20 16:02:47.185][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:47.262][biodb::testThat]
biodb.INFO [2025-12-20 16:02:47.263][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-20 16:02:47.264][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:47.265][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:47.275][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-20 16:02:47.277][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:02:47.278][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-20 16:02:47.280][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-20 16:02:47.282][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-20 16:02:47.283][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:47.344][biodb::testThat]
biodb.INFO [2025-12-20 16:02:47.345][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-20 16:02:47.346][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:47.347][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:47.353][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-20 16:02:47.354][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:02:47.356][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-20 16:02:47.357][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-20 16:02:47.359][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-20 16:02:47.360][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:47.417][biodb::testThat]
biodb.INFO [2025-12-20 16:02:47.418][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-20 16:02:47.419][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:47.421][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:47.483][biodb::testThat]
biodb.INFO [2025-12-20 16:02:47.485][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-20 16:02:47.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:47.487][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:47.544][biodb::testThat]
biodb.INFO [2025-12-20 16:02:47.545][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:47.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:47.548][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:47.609][biodb::testThat]
biodb.INFO [2025-12-20 16:02:47.611][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:47.612][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:47.613][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-12-20 16:02:47.688][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:47.689][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:47.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:47.691][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:47.693][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:47.694][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:47.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:47.696][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:47.698][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:47.699][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:47.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:47.701][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:47.703][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:47.704][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:47.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:47.706][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:47.707][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:47.709][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:47.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:47.711][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:47.712][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:47.714][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:47.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:47.716][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:47.717][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-20 16:02:47.719][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-12-20 16:02:47.720][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-20 16:02:47.721][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:47.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:47.723][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:47.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:47.729][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:47.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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)