Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-04 23:55 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
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 6/29HostnameOS / ArchCHECK
biodbHmdb 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-04 09:55 -0400 (Sat, 04 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 12.7.1 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: 2025-10-04 16:01:15 -0400 (Sat, 04 Oct 2025)
EndedAt: 2025-10-04 16:02:24 -0400 (Sat, 04 Oct 2025)
EllapsedTime: 69.5 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 [2025-10-04 16:02:21.913][biodb::testContext]
biodb.INFO [2025-10-04 16:02:21.916][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:21.917][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-04 16:02:21.917][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:21.918][biodb::testContext]
biodb.INFO [2025-10-04 16:02:21.923][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:21.925][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:21.931][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:21.931][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:02:21.932][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:02:21.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:21.935][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:02:21.949][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:02:21.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:21.952][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:02:21.953][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:02:21.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:21.956][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:02:21.957][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:02:21.966][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:02:21.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.968][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[2025-10-04 16:02:21.969][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:02:21.970][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:02:21.970][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:02:21.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:21.973][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:02:21.975][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:02:21.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.977][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[2025-10-04 16:02:21.978][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:02:21.979][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:02:21.979][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:02:21.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:21.983][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:02:21.984][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:02:21.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:21.987][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:02:21.988][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:02:21.989][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:02:21.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:21.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:21.992][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:21.994][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:02:21.994][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:02:21.995][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:02:21.996][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:02:21.997][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:02:21.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:21.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.001][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:02:22.002][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:02:22.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.006][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:02:22.007][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:02:22.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.011][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:02:22.012][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:02:22.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.015][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:02:22.016][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:02:22.016][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:02:22.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.020][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:22.020][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:02:22.038][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:02:22.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.042][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:02:22.043][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:02:22.043][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:02:22.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.048][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:02:22.072][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.084][self$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[2025-10-04 16:02:22.085][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.086][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:22.087][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.088][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.089][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.089][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.090][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:22.091][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:22.092][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.092][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:02:22.093][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:22.094][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.095][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.095][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:22.095][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:22.095][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:22.095][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:22.095][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:22.096][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:22.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.097][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.098][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:22.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.100][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.101][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:22.102][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:22.103][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.104][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.105][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:02:22.106][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.107][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:22.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.108][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:22.109][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.110][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.111][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.111][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.112][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:22.113][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:22.118][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.119][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:02:22.120][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:22.121][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.122][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.122][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:22.122][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:22.122][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:22.122][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:22.122][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:22.123][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:22.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:22.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.129][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:22.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:22.131][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.132][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.133][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:02:22.134][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.135][self$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[2025-10-04 16:02:22.136][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.137][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:22.138][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.138][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.139][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.140][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.141][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:22.142][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:22.143][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.143][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:02:22.144][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:22.145][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.146][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.147][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.147][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:22.148][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.149][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.150][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:22.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.152][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.153][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.154][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:22.154][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:22.155][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.156][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.157][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:02:22.158][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.159][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:22.160][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.160][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:22.161][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.162][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.163][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.163][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.164][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:22.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:22.166][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.167][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:02:22.167][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:22.168][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.169][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.170][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.171][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:22.171][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.172][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.173][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:22.174][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.175][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.176][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.177][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:22.178][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:22.178][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.179][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.182][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:22.182][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.201][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[2025-10-04 16:02:22.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.208][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[2025-10-04 16:02:22.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.215][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[2025-10-04 16:02:22.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.222][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[2025-10-04 16:02:22.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.226][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[2025-10-04 16:02:22.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.230][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[2025-10-04 16:02:22.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.233][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[2025-10-04 16:02:22.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.237][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[2025-10-04 16:02:22.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.240][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[2025-10-04 16:02:22.241][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:02:22.244][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:02:22.245][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:02:22.246][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:02:22.247][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:02:22.248][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:02:22.253][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:22.255][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:22.256][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:02:22.257][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:02:22.258][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:02:22.259][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:02:22.260][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:22.261][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:22.262][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:22.264][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:22.265][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:02:22.266][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:02:22.267][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:02:22.268][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:02:22.269][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:02:22.270][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:02:22.272][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:02:22.273][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:02:22.274][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:02:22.275][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:02:22.276][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:02:22.277][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:02:22.278][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:02:22.279][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:02:22.280][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:02:22.282][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:02:22.283][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:02:22.284][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:02:22.285][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:02:22.286][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:02:22.287][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:02:22.288][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:02:22.289][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:02:22.290][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:02:22.291][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:02:22.292][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:02:22.294][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:02:22.295][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:02:22.296][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:02:22.297][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:22.298][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:02:22.299][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:02:22.300][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:02:22.302][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:02:22.303][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:02:22.304][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:02:22.305][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:02:22.306][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:02:22.307][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:02:22.309][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:02:22.310][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:02:22.311][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:02:22.312][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:02:22.313][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:02:22.314][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:02:22.315][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:02:22.316][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:02:22.317][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:02:22.319][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:02:22.320][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:02:22.321][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:02:22.322][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:02:22.323][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:02:22.324][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:02:22.325][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:02:22.326][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:02:22.327][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:02:22.328][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:02:22.330][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:02:22.331][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:02:22.332][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:02:22.333][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:02:22.334][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:02:22.335][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:02:22.337][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:02:22.338][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:02:22.339][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:02:22.344][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:02:22.345][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:22.347][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:22.348][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.350][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.358][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[2025-10-04 16:02:22.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.386][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[2025-10-04 16:02:22.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.391][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[2025-10-04 16:02:22.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.396][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[2025-10-04 16:02:22.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.401][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[2025-10-04 16:02:22.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.406][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[2025-10-04 16:02:22.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.411][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[2025-10-04 16:02:22.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.416][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[2025-10-04 16:02:22.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.421][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[2025-10-04 16:02:22.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.426][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[2025-10-04 16:02:22.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.431][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[2025-10-04 16:02:22.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.436][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.WARN [2025-10-04 16:02:22.437][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-10-04 16:02:22.445][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-10-04 16:02:22.456][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-10-04 16:02:22.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:22.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:22.463][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:22.471][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-10-04 16:02:22.472][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.473][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.474][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.475][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:22.475][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.476][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-10-04 16:02:22.477][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.478][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.479][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:22.479][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:22.480][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.481][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-10-04 16:02:22.482][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-10-04 16:02:22.483][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-10-04 16:02:22.484][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:22.485][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:22.485][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-10-04 16:02:22.485][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-10-04 16:02:22.485][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:22.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.487][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:22.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:22.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:22.490][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:22.490][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-10-04 16:02:22.490][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-10-04 16:02:22.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:22.492][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:22.493][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:22.494][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:22.498][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-10-04 16:02:22.500][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:02:22.501][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:02:22.502][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:02:22.503][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:22.526][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-10-04 16:02:22.539][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-10-04 16:02:22.547][biodb::testThat]
biodb.INFO [2025-10-04 16:02:22.548][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-04 16:02:22.548][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:22.549][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:22.552][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[2025-10-04 16:02:22.554][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:02:22.556][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-10-04 16:02:22.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:02:22.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:22.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:22.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:22.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:22.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:22.582][FUN] Functions in observer BiodbConfig: [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[2025-10-04 16:02:22.592][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:22.593][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:22.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.595][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:22.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:22.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.610][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.611][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.613][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.633][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.637][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.638][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.640][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.641][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.644][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.645][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.647][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.648][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.651][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.652][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.654][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.658][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.659][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.661][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.673][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.674][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.676][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.677][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.680][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.681][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.683][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.687][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.688][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.690][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.694][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.695][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.697][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.698][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.702][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:22.703][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:22.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.704][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:22.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:22.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:22.710][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:22.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.711][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:22.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:22.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.716][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.717][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.718][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.723][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.724][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.725][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.730][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:22.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:22.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.732][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:22.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:22.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.737][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:22.738][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:22.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.739][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.740][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:22.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:22.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.744][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:22.745][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:22.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.746][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.747][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:22.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:22.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.751][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-10-04 16:02:22.751][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:22.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.753][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.754][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-10-04 16:02:22.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:22.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:22.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:22.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:22.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:22.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:22.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:22.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.829][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.832][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.835][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:22.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.839][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.842][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.845][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:22.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:22.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:22.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.873][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:22.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.882][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:22.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:22.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:22.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:22.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:22.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:22.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:22.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.894][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:22.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:22.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.897][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:22.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:22.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.900][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:22.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:22.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:22.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:22.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.909][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:22.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:22.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.912][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:22.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:22.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:22.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:22.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:22.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:22.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:22.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:22.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.933][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.936][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.939][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:22.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:22.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:22.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:22.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:22.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:22.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:22.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:22.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.960][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.963][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.965][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:22.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.968][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.971][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.974][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:22.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.977][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:22.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:22.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:22.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:22.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.983][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:22.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:22.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.986][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-04 16:02:22.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:22.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:22.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:22.998][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-04 16:02:23.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.030][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.033][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.036][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.042][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:23.063][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-10-04 16:02:23.065][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:23.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:23.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.068][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:23.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:23.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.071][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:23.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.074][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:23.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:23.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.085][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.116][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.119][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.122][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-04 16:02:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.141][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.142][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.143][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.154][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.157][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.160][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.163][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.164][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.165][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.166][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.186][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.186][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.188][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.199][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.202][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.209][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.212][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.213][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.215][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.216][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.236][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.236][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.238][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.249][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.252][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.255][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.258][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.259][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.261][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.261][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.281][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.281][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.283][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.284][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.293][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:23.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:23.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.296][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:23.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:23.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.299][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:23.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:23.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.302][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:23.303][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:23.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.305][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.305][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:23.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:23.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.319][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:23.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:23.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:23.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:23.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.326][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:23.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:23.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.329][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:23.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:23.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.332][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:23.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:23.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.343][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.346][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.349][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.352][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.353][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.354][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.355][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.374][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.375][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.376][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.387][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.390][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.393][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.396][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.397][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.398][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.399][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.409][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.416][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.423][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.424][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.425][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.426][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.438][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.445][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.446][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.447][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.459][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:23.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:23.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.462][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:23.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:23.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.465][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:23.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:23.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.468][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:23.469][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:23.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.470][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.471][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:23.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:23.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:23.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:23.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:23.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:23.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:23.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:23.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.489][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:23.490][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:23.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.492][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:23.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:23.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.512][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.513][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.514][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.515][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.529][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.532][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.535][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.538][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.539][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.540][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.541][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.552][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:23.552][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:23.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.554][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.558][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.559][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-04 16:02:23.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.561][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.565][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.566][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:02:23.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.567][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.572][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-04 16:02:23.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.574][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.578][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.579][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-04 16:02:23.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.580][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.585][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.585][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:23.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.587][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.591][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.592][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:23.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.593][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.598][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.599][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-04 16:02:23.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.600][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.604][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:23.605][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:23.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.607][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.611][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:23.612][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:23.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.613][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.617][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:23.618][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:23.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.620][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.624][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.625][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:23.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.626][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.630][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.631][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-04 16:02:23.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.632][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.636][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.637][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:23.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.642][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.646][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.647][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.649][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.653][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.654][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:23.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.655][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.659][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.660][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.661][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.666][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-04 16:02:23.666][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-04 16:02:23.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.668][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:23.675][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.675][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-04 16:02:23.676][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:23.677][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:23.687][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-04 16:02:23.690][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:02:23.692][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-04 16:02:23.712][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-04 16:02:23.713][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-04 16:02:23.714][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-04 16:02:23.746][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.747][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-04 16:02:23.747][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:23.748][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:23.750][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.751][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.753][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:23.754][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-10-04 16:02:23.772][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-04 16:02:23.804][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:02:23.805][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-04 16:02:23.806][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-04 16:02:23.807][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-04 16:02:23.820][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-04 16:02:23.839][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.840][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-04 16:02:23.841][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:23.841][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:23.848][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-04 16:02:23.849][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:02:23.850][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-04 16:02:23.851][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-04 16:02:23.852][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-04 16:02:23.853][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-04 16:02:23.863][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.864][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-04 16:02:23.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:23.865][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:23.869][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-04 16:02:23.869][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:02:23.870][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-04 16:02:23.871][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-04 16:02:23.872][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-04 16:02:23.873][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-04 16:02:23.884][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.885][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-04 16:02:23.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:23.886][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.898][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.898][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-04 16:02:23.899][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:23.900][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.915][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.916][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:23.917][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:23.917][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.929][biodb::testThat]
biodb.INFO [2025-10-04 16:02:23.929][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:23.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:23.931][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:23.951][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.952][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.954][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.954][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:23.955][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:23.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.957][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.957][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.958][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.959][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.960][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:23.961][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:23.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.962][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.963][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:23.964][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:23.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.965][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:23.966][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.966][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-04 16:02:23.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:23.968][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:23.969][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:02:23.969][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-10-04 16:02:23.970][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:02:23.971][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:23.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:23.972][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:23.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:23.974][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:23.974][FUN] Functions in observer 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)