Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-27 23:55 -0500 (Sat, 27 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-12-27 09:55 -0500 (Sat, 27 Dec 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-12-27 16:01:29 -0500 (Sat, 27 Dec 2025)
EndedAt: 2025-12-27 16:03:04 -0500 (Sat, 27 Dec 2025)
EllapsedTime: 95.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-12-27 16:02:59.860][biodb::testContext]
biodb.INFO [2025-12-27 16:02:59.864][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-27 16:02:59.865][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-27 16:02:59.866][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-27 16:02:59.867][biodb::testContext]
biodb.INFO [2025-12-27 16:02:59.874][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-27 16:02:59.877][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-27 16:02:59.884][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-27 16:02:59.886][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-27 16:02:59.887][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-27 16:02:59.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.892][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-27 16:02:59.917][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-27 16:02:59.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.922][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-27 16:02:59.923][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-27 16:02:59.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.937][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-27 16:02:59.939][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-27 16:02:59.940][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-27 16:02:59.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.945][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-27 16:02:59.946][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-27 16:02:59.947][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-27 16:02:59.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.952][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-27 16:02:59.953][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-27 16:02:59.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.958][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-27 16:02:59.959][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-27 16:02:59.961][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-27 16:02:59.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.965][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-27 16:02:59.967][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-27 16:02:59.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.971][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-27 16:02:59.973][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-27 16:02:59.974][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-27 16:02:59.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.979][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-27 16:02:59.980][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-27 16:02:59.981][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-27 16:02:59.982][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-27 16:02:59.984][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-27 16:02:59.985][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-27 16:02:59.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.989][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-27 16:02:59.991][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-27 16:02:59.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:02:59.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:02:59.995][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-27 16:02:59.996][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-27 16:02:59.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:02:59.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.000][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[2025-12-27 16:03:00.001][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-27 16:03:00.002][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-27 16:03:00.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.007][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-27 16:03:00.008][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-27 16:03:00.009][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-27 16:03:00.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.014][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-27 16:03:00.016][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-27 16:03:00.026][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-27 16:03:00.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.031][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-27 16:03:00.032][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-27 16:03:00.034][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-27 16:03:00.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.041][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-27 16:03:00.085][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.106][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-27 16:03:00.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-27 16:03:00.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.113][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.115][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-27 16:03:00.117][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-27 16:03:00.118][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.119][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-27 16:03:00.121][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-27 16:03:00.122][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.123][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.124][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-27 16:03:00.124][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-27 16:03:00.124][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-27 16:03:00.124][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-27 16:03:00.124][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-27 16:03:00.126][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-27 16:03:00.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.129][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-27 16:03:00.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.133][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.134][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.135][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-27 16:03:00.137][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-27 16:03:00.138][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.139][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.141][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-27 16:03:00.143][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.144][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-27 16:03:00.145][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.147][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-27 16:03:00.148][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.149][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.150][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.152][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.153][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-27 16:03:00.154][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-27 16:03:00.160][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.161][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-27 16:03:00.163][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-27 16:03:00.164][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.165][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.166][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-27 16:03:00.166][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-27 16:03:00.166][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-27 16:03:00.166][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-27 16:03:00.166][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-27 16:03:00.168][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-27 16:03:00.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.170][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.171][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-27 16:03:00.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.175][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.176][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.177][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-27 16:03:00.178][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-27 16:03:00.179][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.181][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.182][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-27 16:03:00.184][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.186][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-27 16:03:00.187][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.188][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-27 16:03:00.189][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.191][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.192][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.193][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.194][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-27 16:03:00.196][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-27 16:03:00.197][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.198][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-27 16:03:00.199][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-27 16:03:00.201][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.202][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.203][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.204][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-27 16:03:00.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.208][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-27 16:03:00.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.211][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.212][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.214][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-27 16:03:00.215][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-27 16:03:00.216][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.217][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.219][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-27 16:03:00.221][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.222][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-27 16:03:00.223][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-27 16:03:00.226][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.228][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.230][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.231][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-27 16:03:00.232][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-27 16:03:00.233][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.235][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-27 16:03:00.236][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-27 16:03:00.237][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.239][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.240][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.241][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-27 16:03:00.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.245][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-27 16:03:00.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.249][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.251][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-27 16:03:00.252][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-27 16:03:00.253][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.254][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.258][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-27 16:03:00.260][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.352][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-27 16:03:00.357][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-27 16:03:00.359][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-27 16:03:00.361][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-27 16:03:00.363][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-27 16:03:00.365][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-27 16:03:00.367][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-27 16:03:00.373][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-27 16:03:00.375][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-27 16:03:00.377][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-27 16:03:00.379][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-27 16:03:00.380][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-27 16:03:00.382][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-27 16:03:00.384][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-27 16:03:00.386][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-27 16:03:00.388][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-27 16:03:00.389][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-27 16:03:00.391][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-27 16:03:00.393][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-27 16:03:00.395][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-27 16:03:00.396][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-27 16:03:00.398][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-27 16:03:00.400][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-27 16:03:00.402][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-27 16:03:00.404][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-27 16:03:00.406][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-27 16:03:00.408][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-27 16:03:00.409][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-27 16:03:00.411][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-27 16:03:00.413][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-27 16:03:00.415][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-27 16:03:00.417][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-27 16:03:00.418][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-27 16:03:00.420][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-27 16:03:00.422][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-27 16:03:00.424][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-27 16:03:00.426][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-27 16:03:00.428][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-27 16:03:00.430][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-27 16:03:00.432][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-27 16:03:00.434][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-27 16:03:00.436][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-27 16:03:00.438][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-27 16:03:00.440][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-27 16:03:00.442][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-27 16:03:00.443][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-27 16:03:00.445][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-27 16:03:00.447][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-27 16:03:00.449][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-27 16:03:00.450][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-27 16:03:00.452][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-27 16:03:00.454][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-27 16:03:00.456][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-27 16:03:00.457][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-27 16:03:00.459][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-27 16:03:00.461][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-27 16:03:00.463][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-27 16:03:00.465][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-27 16:03:00.466][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-27 16:03:00.468][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-27 16:03:00.470][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-27 16:03:00.472][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-27 16:03:00.474][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-27 16:03:00.476][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-27 16:03:00.478][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-27 16:03:00.479][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-27 16:03:00.481][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-27 16:03:00.483][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-27 16:03:00.485][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-27 16:03:00.486][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-27 16:03:00.488][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-27 16:03:00.490][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-27 16:03:00.492][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-27 16:03:00.493][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-27 16:03:00.495][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-27 16:03:00.497][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-27 16:03:00.499][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-27 16:03:00.500][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-27 16:03:00.502][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-27 16:03:00.504][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-27 16:03:00.506][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-27 16:03:00.507][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-27 16:03:00.509][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-27 16:03:00.517][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-27 16:03:00.519][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-27 16:03:00.523][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-27 16:03:00.524][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.527][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.582][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.DEBUG[2025-12-27 16:03:00.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-12-27 16:03:00.674][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-12-27 16:03:00.684][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-12-27 16:03:00.703][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-12-27 16:03:00.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-27 16:03:00.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-27 16:03:00.714][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-12-27 16:03:00.726][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-12-27 16:03:00.729][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.730][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.731][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.733][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-27 16:03:00.734][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.735][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-12-27 16:03:00.736][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.738][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.739][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-27 16:03:00.740][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-27 16:03:00.741][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.743][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-12-27 16:03:00.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-12-27 16:03:00.745][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-12-27 16:03:00.747][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-27 16:03:00.748][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-27 16:03:00.748][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-12-27 16:03:00.748][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-12-27 16:03:00.749][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-27 16:03:00.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.753][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-27 16:03:00.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-27 16:03:00.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-27 16:03:00.756][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-27 16:03:00.757][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-12-27 16:03:00.757][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-12-27 16:03:00.759][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-27 16:03:00.760][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-27 16:03:00.761][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-27 16:03:00.762][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-27 16:03:00.770][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-12-27 16:03:00.772][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-27 16:03:00.774][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-27 16:03:00.776][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-27 16:03:00.778][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-27 16:03:00.805][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-12-27 16:03:00.820][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-12-27 16:03:00.833][biodb::testThat]
biodb.INFO [2025-12-27 16:03:00.834][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-27 16:03:00.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:00.837][biodb::testThat]
biodb.TRACE[2025-12-27 16:03:00.842][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-12-27 16:03:00.844][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-12-27 16:03:00.848][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-12-27 16:03:00.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-27 16:03:00.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:00.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:00.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:00.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:00.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:00.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-27 16:03:00.892][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:00.894][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:00.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.896][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:00.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:00.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.920][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:00.922][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:00.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.925][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.962][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:00.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:00.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.968][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:00.970][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:00.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.972][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.975][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:00.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:00.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.982][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:00.983][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:00.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.986][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.988][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:00.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:00.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.993][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:00.994][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:00.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:00.997][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:00.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:01.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:01.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.004][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.005][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.007][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.023][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.025][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.027][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.029][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.034][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.035][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.038][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.039][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.044][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.046][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.048][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.050][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.055][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.056][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.059][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.060][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.065][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:01.067][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:01.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.069][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:01.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:01.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.076][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:01.077][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:01.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.080][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:01.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:01.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.087][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.088][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.090][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.097][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.099][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.101][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.108][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.110][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.112][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.114][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.119][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:01.120][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:01.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.123][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.124][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:01.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:01.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.129][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:01.131][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:01.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.133][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:01.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:01.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.140][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-12-27 16:03:01.142][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:01.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.144][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.146][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-12-27 16:03:01.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:01.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.271][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:01.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:01.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.276][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:01.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:01.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.282][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:01.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:01.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.287][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:01.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:01.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.292][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:01.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:01.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.297][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:01.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:01.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:01.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:01.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:01.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:01.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:01.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:01.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.341][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.348][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.353][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:01.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.358][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.364][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.369][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:01.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:01.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:01.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.383][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:01.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:01.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.389][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:01.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:01.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.394][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:01.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:01.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.400][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:01.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:01.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.405][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:01.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:01.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.411][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:01.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:01.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:01.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:01.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.429][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:01.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:01.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:01.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:01.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:01.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:01.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:01.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:01.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.475][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.481][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.487][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:01.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:01.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.529][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.534][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:01.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.539][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.545][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.552][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.557][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:01.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:01.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.563][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:01.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:01.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:01.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:01.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.573][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-27 16:03:01.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.593][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-27 16:03:01.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:01.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:01.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:01.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.653][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.658][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.668][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-27 16:03:01.703][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-12-27 16:03:01.706][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-27 16:03:01.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-27 16:03:01.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.711][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-27 16:03:01.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-27 16:03:01.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.716][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-27 16:03:01.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-27 16:03:01.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.721][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-27 16:03:01.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-27 16:03:01.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.787][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.859][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.865][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.870][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-27 16:03:01.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.903][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.906][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.910][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:01.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:01.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.928][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.934][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.940][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.946][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.947][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.949][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.951][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:01.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.981][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.983][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.985][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:01.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:01.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:01.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.012][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.017][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.022][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.027][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.028][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.031][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.032][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.070][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.071][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.074][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.090][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.096][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.101][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.108][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.110][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.115][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.117][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:02.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:02.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:02.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:02.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:02.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:02.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.153][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:02.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:02.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.157][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:02.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:02.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:02.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:02.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.181][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:02.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:02.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.187][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:02.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:02.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.192][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:02.194][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:02.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.196][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.197][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:02.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:02.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:02.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:02.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:02.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:02.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:02.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:02.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.236][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:02.238][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:02.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.240][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:02.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:02.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.260][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.265][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.270][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.277][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.278][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.282][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.285][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.329][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.330][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.333][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.354][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.359][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.365][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.370][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.371][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.374][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.375][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.391][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.402][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.407][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.408][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.411][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.443][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.448][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.449][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.452][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.453][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.473][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:02.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:02.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:02.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:02.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.485][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:02.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:02.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.490][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:02.492][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:02.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.494][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.496][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:02.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:02.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:02.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:02.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:02.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:02.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:02.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:02.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.528][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:02.530][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:02.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.532][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:02.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:02.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.564][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.565][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.568][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.569][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.585][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.590][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.595][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.605][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.607][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.609][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.610][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.628][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-27 16:03:02.629][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-27 16:03:02.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.632][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.638][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.640][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-27 16:03:02.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.642][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.649][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.651][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-27 16:03:02.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.653][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.660][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.661][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-27 16:03:02.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.664][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.670][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:02.672][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-27 16:03:02.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.674][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.681][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.683][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-27 16:03:02.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.685][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.692][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.693][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-27 16:03:02.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.696][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.702][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.704][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-27 16:03:02.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.706][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.713][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:02.714][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:02.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.717][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.723][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-27 16:03:02.724][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-27 16:03:02.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.727][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-27 16:03:02.735][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-27 16:03:02.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.737][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.744][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.745][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-27 16:03:02.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.748][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.754][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.756][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-27 16:03:02.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.758][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.765][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.767][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-27 16:03:02.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.769][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.776][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:02.778][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:02.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.780][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.787][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.794][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-27 16:03:02.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.796][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.804][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:02.805][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:02.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.808][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:02.814][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-27 16:03:02.816][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-27 16:03:02.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:02.818][ef$get] fields variable is a list.
biodb.INFO [2025-12-27 16:03:02.829][biodb::testThat]
biodb.INFO [2025-12-27 16:03:02.832][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-27 16:03:02.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:02.838][biodb::testThat]
biodb.DEBUG[2025-12-27 16:03:02.871][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-27 16:03:02.876][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-27 16:03:02.882][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-27 16:03:02.949][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-27 16:03:02.951][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-27 16:03:02.953][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-27 16:03:03.149][biodb::testThat]
biodb.INFO [2025-12-27 16:03:03.150][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-27 16:03:03.152][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:03.153][biodb::testThat]
biodb.TRACE[2025-12-27 16:03:03.158][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:03.160][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:03.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:03.167][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-27 16:03:03.169][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-12-27 16:03:03.199][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-27 16:03:03.264][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-27 16:03:03.266][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-27 16:03:03.267][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-27 16:03:03.269][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-27 16:03:03.286][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-27 16:03:03.364][biodb::testThat]
biodb.INFO [2025-12-27 16:03:03.365][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-27 16:03:03.366][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:03.368][biodb::testThat]
biodb.DEBUG[2025-12-27 16:03:03.377][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-27 16:03:03.379][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-27 16:03:03.381][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-27 16:03:03.382][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-27 16:03:03.384][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-27 16:03:03.385][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-27 16:03:03.447][biodb::testThat]
biodb.INFO [2025-12-27 16:03:03.448][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-27 16:03:03.449][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:03.450][biodb::testThat]
biodb.DEBUG[2025-12-27 16:03:03.455][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-27 16:03:03.456][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-27 16:03:03.458][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-27 16:03:03.460][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-27 16:03:03.461][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-27 16:03:03.462][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-27 16:03:03.520][biodb::testThat]
biodb.INFO [2025-12-27 16:03:03.521][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-27 16:03:03.522][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:03.524][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-27 16:03:03.586][biodb::testThat]
biodb.INFO [2025-12-27 16:03:03.587][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-27 16:03:03.588][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:03.590][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-27 16:03:03.647][biodb::testThat]
biodb.INFO [2025-12-27 16:03:03.649][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-27 16:03:03.650][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:03.651][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-27 16:03:03.713][biodb::testThat]
biodb.INFO [2025-12-27 16:03:03.714][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-27 16:03:03.716][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-27 16:03:03.717][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-12-27 16:03:03.792][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:03.794][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:03.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:03.796][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:03.797][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:03.799][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:03.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:03.801][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:03.802][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:03.804][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:03.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:03.806][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:03.807][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-27 16:03:03.809][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-27 16:03:03.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:03.811][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:03.812][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-27 16:03:03.813][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-27 16:03:03.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:03.816][ef$get] fields variable is a list.
biodb.TRACE[2025-12-27 16:03:03.817][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:03.818][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-27 16:03:03.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-27 16:03:03.821][ef$get] fields variable is a list.
biodb.INFO [2025-12-27 16:03:03.822][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-27 16:03:03.823][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-12-27 16:03:03.824][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-27 16:03:03.825][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-27 16:03:03.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-27 16:03:03.828][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-27 16:03:03.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-27 16:03:03.834][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-27 16:03:03.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

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