Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-18 23:55 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
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 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-18 09:55 -0400 (Sat, 18 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: fa89c02
git_last_commit_date: 2025-07-24 10:45:35 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on lconway

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: 1.15.1
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_1.15.1.tar.gz
StartedAt: 2025-10-18 16:01:15 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 16:02:20 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 65.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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 [2025-10-18 16:02:16.917][biodb::testContext]
biodb.INFO [2025-10-18 16:02:16.920][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:16.921][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-18 16:02:16.922][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-18 16:02:16.923][biodb::testContext]
biodb.INFO [2025-10-18 16:02:16.928][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:16.929][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:16.935][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:16.936][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-18 16:02:16.937][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-18 16:02:16.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:16.940][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-18 16:02:16.953][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-18 16:02:16.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:16.956][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-18 16:02:16.957][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-18 16:02:16.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:16.969][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-18 16:02:16.969][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-18 16:02:16.970][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-18 16:02:16.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.972][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[2025-10-18 16:02:16.973][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-18 16:02:16.974][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-18 16:02:16.975][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-18 16:02:16.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:16.977][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-18 16:02:16.978][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-18 16:02:16.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.980][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[2025-10-18 16:02:16.981][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-18 16:02:16.982][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-18 16:02:16.983][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-18 16:02:16.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:16.986][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-18 16:02:16.987][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-18 16:02:16.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:16.990][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-18 16:02:16.991][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-18 16:02:16.992][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-18 16:02:16.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:16.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:16.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:16.994][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:16.995][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-18 16:02:16.996][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-18 16:02:16.997][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-18 16:02:16.998][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-18 16:02:16.998][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-18 16:02:16.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.001][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-18 16:02:17.002][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-18 16:02:17.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.005][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-18 16:02:17.006][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-18 16:02:17.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.009][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-18 16:02:17.010][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-18 16:02:17.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.013][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-18 16:02:17.013][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-18 16:02:17.014][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-18 16:02:17.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.016][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[2025-10-18 16:02:17.017][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-18 16:02:17.018][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-18 16:02:17.038][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-18 16:02:17.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.042][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-18 16:02:17.042][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-18 16:02:17.043][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-18 16:02:17.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.048][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-18 16:02:17.073][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.086][self$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[2025-10-18 16:02:17.087][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.088][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:17.089][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.090][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.091][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.091][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.092][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:17.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:17.094][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.095][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-18 16:02:17.095][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:17.096][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.097][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.098][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:17.098][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:17.098][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:17.098][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:17.098][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:17.099][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:17.100][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.100][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.101][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:17.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.104][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.105][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.105][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:17.106][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:17.107][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.108][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.109][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-18 16:02:17.110][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.111][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:17.112][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.113][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:17.118][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.119][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.120][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.121][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.121][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:17.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:17.123][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.124][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-18 16:02:17.125][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:17.125][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.126][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.127][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:17.127][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-18 16:02:17.127][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-18 16:02:17.127][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-18 16:02:17.127][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-18 16:02:17.128][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:17.129][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.130][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:17.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.133][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.134][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.134][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:17.135][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:17.136][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.137][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.138][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-18 16:02:17.139][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.140][self$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[2025-10-18 16:02:17.141][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.142][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:17.143][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.144][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.144][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.145][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.146][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-18 16:02:17.147][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:17.148][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.149][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-18 16:02:17.150][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:17.151][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.151][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.152][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.153][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:17.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.155][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:17.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.157][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.158][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:17.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:17.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.161][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.162][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-18 16:02:17.163][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.164][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-18 16:02:17.165][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.166][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:17.167][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.168][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.168][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.169][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.170][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-18 16:02:17.171][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:17.172][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.173][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-18 16:02:17.174][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:17.174][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.175][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.176][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.177][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-18 16:02:17.178][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.179][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:17.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.181][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.182][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.183][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:17.184][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:17.184][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.185][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.188][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:17.189][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.248][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-18 16:02:17.255][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-18 16:02:17.256][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-18 16:02:17.257][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-18 16:02:17.259][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-18 16:02:17.260][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-18 16:02:17.261][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:17.262][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:17.263][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-18 16:02:17.264][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-18 16:02:17.265][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-18 16:02:17.266][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-18 16:02:17.267][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-18 16:02:17.268][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-18 16:02:17.269][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-18 16:02:17.270][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:17.271][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-18 16:02:17.272][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-18 16:02:17.273][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-18 16:02:17.275][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-18 16:02:17.276][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-18 16:02:17.277][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-18 16:02:17.278][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-18 16:02:17.279][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-18 16:02:17.280][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-18 16:02:17.281][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-18 16:02:17.283][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-18 16:02:17.284][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-18 16:02:17.285][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-18 16:02:17.286][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-18 16:02:17.287][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-18 16:02:17.288][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-18 16:02:17.289][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-18 16:02:17.290][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-18 16:02:17.291][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-18 16:02:17.292][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-18 16:02:17.294][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-18 16:02:17.295][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-18 16:02:17.296][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-18 16:02:17.297][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-18 16:02:17.298][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-18 16:02:17.299][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-18 16:02:17.300][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-18 16:02:17.301][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-18 16:02:17.303][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-18 16:02:17.304][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-18 16:02:17.305][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-18 16:02:17.306][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-18 16:02:17.307][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-18 16:02:17.308][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-18 16:02:17.309][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-18 16:02:17.311][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-18 16:02:17.312][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-18 16:02:17.313][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-18 16:02:17.314][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-18 16:02:17.315][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-18 16:02:17.316][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-18 16:02:17.317][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-18 16:02:17.319][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-18 16:02:17.320][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-18 16:02:17.321][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-18 16:02:17.323][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-18 16:02:17.324][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-18 16:02:17.325][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-18 16:02:17.326][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-18 16:02:17.327][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-18 16:02:17.329][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-18 16:02:17.330][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-18 16:02:17.331][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-18 16:02:17.332][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-18 16:02:17.333][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-18 16:02:17.334][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-18 16:02:17.335][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-18 16:02:17.337][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-18 16:02:17.338][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-18 16:02:17.339][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-18 16:02:17.340][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-18 16:02:17.341][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-18 16:02:17.342][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-18 16:02:17.343][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-18 16:02:17.344][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-18 16:02:17.345][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-18 16:02:17.346][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-18 16:02:17.351][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-18 16:02:17.352][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-18 16:02:17.355][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-18 16:02:17.356][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.357][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.446][FUN] Functions in observer BiodbConfig: [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 [2025-10-18 16:02:17.447][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-10-18 16:02:17.454][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-10-18 16:02:17.466][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-10-18 16:02:17.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-18 16:02:17.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-18 16:02:17.473][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-10-18 16:02:17.481][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-10-18 16:02:17.483][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.484][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.485][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.486][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-18 16:02:17.487][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.487][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-10-18 16:02:17.488][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.489][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.490][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-18 16:02:17.491][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-18 16:02:17.492][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.492][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-10-18 16:02:17.493][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-10-18 16:02:17.494][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-10-18 16:02:17.495][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-18 16:02:17.497][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-18 16:02:17.497][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-10-18 16:02:17.497][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-10-18 16:02:17.497][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-18 16:02:17.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.500][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-18 16:02:17.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-18 16:02:17.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-18 16:02:17.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-18 16:02:17.503][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-10-18 16:02:17.503][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-10-18 16:02:17.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-18 16:02:17.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-18 16:02:17.506][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-18 16:02:17.506][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-18 16:02:17.516][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-10-18 16:02:17.517][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-18 16:02:17.519][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-18 16:02:17.520][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-18 16:02:17.521][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-18 16:02:17.541][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-10-18 16:02:17.555][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-10-18 16:02:17.562][biodb::testThat]
biodb.INFO [2025-10-18 16:02:17.563][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-18 16:02:17.564][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:17.565][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:17.569][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[2025-10-18 16:02:17.570][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-10-18 16:02:17.573][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-10-18 16:02:17.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-18 16:02:17.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:17.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:17.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:17.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:17.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:17.595][FUN] Functions in observer BiodbConfig: [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[2025-10-18 16:02:17.604][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:17.605][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:17.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.606][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:17.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:17.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.621][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.622][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.624][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.644][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.649][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.649][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.651][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.652][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.656][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.657][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.659][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.660][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.674][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.675][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.677][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.681][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.682][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.684][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.688][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.689][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.690][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.691][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.695][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.696][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.697][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.698][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.702][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.702][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.704][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.705][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.708][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.709][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.711][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.715][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:17.716][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:17.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.717][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:17.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:17.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.721][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:17.722][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:17.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.724][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:17.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:17.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.728][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.729][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.730][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.734][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.735][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.736][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.740][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:17.741][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:17.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.743][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:17.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:17.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.746][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:17.747][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:17.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.749][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.750][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:17.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:17.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.753][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:17.753][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:17.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.755][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.756][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:17.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:17.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.759][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-10-18 16:02:17.760][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:17.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.761][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.762][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-10-18 16:02:17.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:17.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:17.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:17.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:17.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:17.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:17.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:17.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.835][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.839][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.842][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:17.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.845][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.848][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.852][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:17.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:17.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:17.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.873][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:17.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.882][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:17.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.894][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:17.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:17.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:17.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.903][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:17.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:17.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.906][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:17.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:17.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.909][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:17.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:17.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.912][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:17.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:17.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.915][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:17.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:17.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:17.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:17.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.921][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:17.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:17.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:17.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:17.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:17.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:17.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.942][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.945][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:17.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:17.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:17.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:17.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:17.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:17.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:17.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:17.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.969][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:17.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.975][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.978][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:17.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.984][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:17.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:17.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.987][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:17.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:17.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.990][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:17.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:17.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.993][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-18 16:02:17.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:17.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:17.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:17.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.008][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-18 16:02:18.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.041][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.044][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.050][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:18.073][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-10-18 16:02:18.076][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:18.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:18.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-18 16:02:18.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-18 16:02:18.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.082][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:18.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-18 16:02:18.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.084][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-18 16:02:18.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.100][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.129][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.132][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.136][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-18 16:02:18.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.155][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.155][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.157][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.168][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.171][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.177][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.178][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.179][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.180][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.200][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.200][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.206][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.219][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.222][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.226][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.229][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.230][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.232][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.233][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.253][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.254][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.255][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.266][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.270][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.273][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.276][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.277][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.278][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.279][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.299][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.300][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.301][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.313][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:18.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:18.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:18.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:18.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.324][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:18.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:18.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.327][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:18.328][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:18.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.330][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.331][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:18.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.342][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:18.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:18.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:18.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:18.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.349][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:18.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:18.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.353][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:18.354][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:18.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.355][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:18.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:18.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.369][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.374][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.379][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.383][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.384][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.386][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.387][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.409][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.410][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.412][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.427][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.430][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.433][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.434][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.435][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.436][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.451][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.454][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.460][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.461][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.463][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.482][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.483][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.484][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.495][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:18.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:18.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.498][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:18.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:18.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.501][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:18.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:18.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.504][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:18.505][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:18.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.506][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.507][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:18.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:18.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:18.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.520][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:18.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:18.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:18.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:18.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.526][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:18.526][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:18.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.528][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:18.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:18.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.551][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.551][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.553][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.563][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.566][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.569][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.572][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.573][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.574][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.575][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.585][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-18 16:02:18.585][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-18 16:02:18.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.587][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.591][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.592][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-18 16:02:18.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.593][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.597][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.598][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-18 16:02:18.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.599][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.604][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.604][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-18 16:02:18.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.606][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.610][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.611][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-18 16:02:18.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.612][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.616][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.617][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-18 16:02:18.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.618][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.622][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.623][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-18 16:02:18.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.624][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.629][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.630][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-18 16:02:18.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.631][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.635][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:18.636][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:18.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.637][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.642][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-18 16:02:18.642][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-18 16:02:18.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.644][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.652][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-18 16:02:18.653][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-18 16:02:18.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.655][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.659][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.660][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-18 16:02:18.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.661][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.665][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.666][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-18 16:02:18.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.667][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.671][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.672][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-18 16:02:18.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.673][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.677][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.678][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.680][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.684][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.684][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-18 16:02:18.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.686][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.690][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.691][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.692][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.696][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-18 16:02:18.697][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-18 16:02:18.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.698][ef$get] fields variable is a list.
biodb.INFO [2025-10-18 16:02:18.705][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.706][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-18 16:02:18.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:18.707][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:18.718][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-18 16:02:18.721][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-18 16:02:18.723][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-18 16:02:18.742][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-18 16:02:18.748][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-18 16:02:18.748][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-18 16:02:18.777][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.778][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-18 16:02:18.779][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:18.780][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:18.782][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.783][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.784][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-18 16:02:18.785][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-10-18 16:02:18.802][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-18 16:02:18.841][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-18 16:02:18.842][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-18 16:02:18.843][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-18 16:02:18.844][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-18 16:02:18.852][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-18 16:02:18.871][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.872][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-18 16:02:18.872][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:18.873][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:18.880][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-18 16:02:18.880][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-18 16:02:18.882][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-18 16:02:18.883][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-18 16:02:18.884][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-18 16:02:18.884][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-18 16:02:18.896][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.897][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-18 16:02:18.898][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:18.898][biodb::testThat]
biodb.DEBUG[2025-10-18 16:02:18.902][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-18 16:02:18.903][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-18 16:02:18.904][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-18 16:02:18.905][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-18 16:02:18.906][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-18 16:02:18.907][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-18 16:02:18.918][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.919][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-18 16:02:18.920][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:18.925][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.936][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.937][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-18 16:02:18.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:18.938][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.950][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.950][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:18.951][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:18.952][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.963][biodb::testThat]
biodb.INFO [2025-10-18 16:02:18.964][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-18 16:02:18.965][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-18 16:02:18.965][biodb::testThat]
biodb.TRACE[2025-10-18 16:02:18.985][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.986][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.988][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.989][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:18.989][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:18.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.991][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.992][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.992][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:18.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.994][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.995][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-18 16:02:18.995][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-18 16:02:18.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:18.997][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:18.997][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-18 16:02:18.998][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-18 16:02:18.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:19.000][ef$get] fields variable is a list.
biodb.TRACE[2025-10-18 16:02:19.001][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:19.002][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-18 16:02:19.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-18 16:02:19.003][ef$get] fields variable is a list.
biodb.INFO [2025-10-18 16:02:19.004][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-18 16:02:19.005][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-10-18 16:02:19.005][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-18 16:02:19.006][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-18 16:02:19.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-18 16:02:19.007][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-18 16:02:19.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-18 16:02:19.008][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-18 16:02:19.013][FUN] Functions in observer 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 0 | PASS 103 ]

══ 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 0 | 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_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.15.1’
* 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:
   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 0 | 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 ‘1.15.1’
** 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)