Back to Long Tests report for BioC 3.22

This page was generated on 2026-01-24 23:55 -0500 (Sat, 24 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4886
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4676
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-01-24 09:55 -0500 (Sat, 24 Jan 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-01-24 16:01:31 -0500 (Sat, 24 Jan 2026)
EndedAt: 2026-01-24 16:02:59 -0500 (Sat, 24 Jan 2026)
EllapsedTime: 88.3 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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2026-01-24 16:02:54.792][biodb::testContext]
biodb.INFO [2026-01-24 16:02:54.796][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:54.798][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-01-24 16:02:54.799][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:54.800][biodb::testContext]
biodb.INFO [2026-01-24 16:02:54.807][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:54.809][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:54.816][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:54.818][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-24 16:02:54.819][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-24 16:02:54.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.824][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-24 16:02:54.849][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-24 16:02:54.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.854][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-24 16:02:54.856][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-24 16:02:54.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.860][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-24 16:02:54.862][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-24 16:02:54.863][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-24 16:02:54.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.867][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-24 16:02:54.869][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-24 16:02:54.870][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-24 16:02:54.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.875][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-24 16:02:54.876][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-24 16:02:54.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.880][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-24 16:02:54.882][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-24 16:02:54.883][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-24 16:02:54.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.887][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-24 16:02:54.889][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-24 16:02:54.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.893][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-24 16:02:54.895][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-24 16:02:54.896][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-24 16:02:54.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.900][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:54.902][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-24 16:02:54.903][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-24 16:02:54.904][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-24 16:02:54.905][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-24 16:02:54.907][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-24 16:02:54.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.911][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-24 16:02:54.913][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-24 16:02:54.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.917][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-24 16:02:54.918][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-24 16:02:54.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.923][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-24 16:02:54.924][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-24 16:02:54.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.929][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-24 16:02:54.930][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-24 16:02:54.931][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-24 16:02:54.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.936][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:54.937][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-24 16:02:54.948][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-24 16:02:54.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.953][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-24 16:02:54.954][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-24 16:02:54.956][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-24 16:02:54.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:54.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:54.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:54.963][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-24 16:02:55.010][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.039][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-24 16:02:55.041][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.043][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:55.044][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.045][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.047][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.048][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.049][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:55.050][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:55.052][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.053][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-24 16:02:55.054][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:55.055][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.057][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.058][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:55.058][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:55.058][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:55.058][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:55.058][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:55.059][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:55.061][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.063][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:55.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.067][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.068][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.069][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:55.070][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:55.072][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.073][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.074][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-24 16:02:55.077][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.078][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:55.079][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.080][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:55.082][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.083][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.084][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.085][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.086][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:55.088][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:55.089][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.090][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-24 16:02:55.091][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:55.093][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.094][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.095][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:55.095][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:55.095][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:55.095][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:55.095][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:55.096][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:55.098][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.100][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:55.101][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.103][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.105][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.106][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:55.107][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:55.108][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.109][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.111][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-24 16:02:55.113][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.114][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-24 16:02:55.115][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.117][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:55.118][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.119][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.120][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.121][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.123][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:55.124][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:55.125][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.126][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-24 16:02:55.128][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:55.129][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.130][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.131][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.132][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:55.134][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.136][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:55.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.141][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.142][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:55.143][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:55.144][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.145][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.147][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-24 16:02:55.149][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.150][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:55.151][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:55.154][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.155][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.156][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.158][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.159][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:55.160][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:55.161][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.162][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-24 16:02:55.164][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:55.165][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.166][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.167][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.169][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:55.170][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.172][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:55.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.175][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.177][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.178][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:55.179][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:55.180][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.181][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.185][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:55.186][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.272][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[2026-01-24 16:02:55.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.278][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[2026-01-24 16:02:55.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.292][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-24 16:02:55.296][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-24 16:02:55.298][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-24 16:02:55.300][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-24 16:02:55.302][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-24 16:02:55.303][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-24 16:02:55.305][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:55.307][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:55.309][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-24 16:02:55.310][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-24 16:02:55.312][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-24 16:02:55.314][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-24 16:02:55.315][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:55.317][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:55.319][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:55.320][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:55.322][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-24 16:02:55.324][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-24 16:02:55.326][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-24 16:02:55.327][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-24 16:02:55.329][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-24 16:02:55.331][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-24 16:02:55.332][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-24 16:02:55.334][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-24 16:02:55.336][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-24 16:02:55.338][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-24 16:02:55.339][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-24 16:02:55.341][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-24 16:02:55.343][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-24 16:02:55.344][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-24 16:02:55.346][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-24 16:02:55.348][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-24 16:02:55.350][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-24 16:02:55.352][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-24 16:02:55.353][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-24 16:02:55.355][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-24 16:02:55.357][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-24 16:02:55.358][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-24 16:02:55.360][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-24 16:02:55.362][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-24 16:02:55.363][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-24 16:02:55.365][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-24 16:02:55.367][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-24 16:02:55.369][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-24 16:02:55.370][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-24 16:02:55.372][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:55.374][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-24 16:02:55.375][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-24 16:02:55.377][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-24 16:02:55.379][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-24 16:02:55.380][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-24 16:02:55.382][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-24 16:02:55.384][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-24 16:02:55.386][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-24 16:02:55.387][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-24 16:02:55.389][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-24 16:02:55.391][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-24 16:02:55.393][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-24 16:02:55.394][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-24 16:02:55.396][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-24 16:02:55.398][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-24 16:02:55.399][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-24 16:02:55.401][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-24 16:02:55.403][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-24 16:02:55.404][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-24 16:02:55.406][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-24 16:02:55.408][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-24 16:02:55.410][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-24 16:02:55.411][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-24 16:02:55.413][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-24 16:02:55.415][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-24 16:02:55.416][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-24 16:02:55.418][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-24 16:02:55.420][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-24 16:02:55.421][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-24 16:02:55.423][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-24 16:02:55.425][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-24 16:02:55.427][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-24 16:02:55.428][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-24 16:02:55.430][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-24 16:02:55.432][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-24 16:02:55.433][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-24 16:02:55.435][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-24 16:02:55.443][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-24 16:02:55.445][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:55.449][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:55.450][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.452][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2026-01-24 16:02:55.589][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-01-24 16:02:55.599][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-01-24 16:02:55.617][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-01-24 16:02:55.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:55.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:55.628][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:55.640][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-01-24 16:02:55.643][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.644][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.645][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.647][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:55.648][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.649][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-01-24 16:02:55.650][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.653][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:55.654][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:55.655][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.657][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-01-24 16:02:55.658][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-01-24 16:02:55.659][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-01-24 16:02:55.661][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:55.662][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:55.662][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-01-24 16:02:55.662][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-01-24 16:02:55.663][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:55.665][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.666][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.667][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:55.668][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:55.669][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:55.670][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:55.672][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-01-24 16:02:55.672][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-01-24 16:02:55.673][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:55.674][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:55.675][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:55.676][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:55.684][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-01-24 16:02:55.686][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-24 16:02:55.688][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-24 16:02:55.690][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-24 16:02:55.692][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:55.714][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-01-24 16:02:55.729][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-01-24 16:02:55.739][biodb::testThat]
biodb.INFO [2026-01-24 16:02:55.740][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-24 16:02:55.742][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:55.743][biodb::testThat]
biodb.TRACE[2026-01-24 16:02:55.748][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-01-24 16:02:55.750][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-01-24 16:02:55.755][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-01-24 16:02:55.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-24 16:02:55.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:55.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:55.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:55.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:55.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:55.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-24 16:02:55.797][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:55.798][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:55.800][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.801][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:55.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:55.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.834][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:55.835][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:55.836][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.837][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.873][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:55.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:55.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.878][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:55.880][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:55.881][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.882][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.884][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:55.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:55.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.889][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:55.890][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:55.891][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.892][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.894][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:55.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:55.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.899][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:55.900][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:55.901][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.903][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:55.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:55.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.909][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:55.911][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:55.912][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.913][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:55.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:55.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.920][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:55.921][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:55.922][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.923][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.925][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:55.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:55.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.930][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:55.931][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:55.932][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.933][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.935][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:55.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:55.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.940][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:55.941][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:55.943][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.944][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.945][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:55.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.950][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:55.952][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:55.953][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.954][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.955][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:55.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:55.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.960][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:55.962][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:55.963][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.964][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.965][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:55.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:55.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.970][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:55.972][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:55.973][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.974][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:55.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:55.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.981][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:55.982][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:55.983][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.984][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:55.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:55.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.991][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:55.992][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:55.993][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:55.995][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:55.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:55.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:55.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.001][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.002][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.004][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.005][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.011][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.013][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.014][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.015][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.016][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.025][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:56.027][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:56.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.029][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.030][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:56.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:56.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.035][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-01-24 16:02:56.037][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:56.038][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.039][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.041][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-01-24 16:02:56.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:56.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.110][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:56.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:56.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.115][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:56.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:56.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.120][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:56.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:56.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.125][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:56.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:56.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.130][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:56.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:56.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.135][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:56.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:56.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.170][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:56.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:56.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:56.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:56.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.180][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:56.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:56.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.185][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:56.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:56.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.190][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:56.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:56.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.196][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:56.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:56.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.207][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:56.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:56.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:56.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:56.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.217][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.222][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.227][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.232][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:56.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:56.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:56.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:56.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.246][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:56.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:56.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:56.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:56.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:56.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:56.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:56.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:56.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.282][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.287][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.292][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:56.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:56.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:56.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:56.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:56.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:56.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.327][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.332][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.337][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.342][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.347][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.352][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.357][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:56.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:56.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.362][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:56.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:56.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.367][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:56.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.372][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-24 16:02:56.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.392][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-24 16:02:56.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:56.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.440][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.496][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.505][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.519][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:56.560][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-01-24 16:02:56.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:56.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:56.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.573][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:56.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:56.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:56.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:56.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.586][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:56.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:56.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.607][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-24 16:02:56.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.694][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.695][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.697][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.698][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:56.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:56.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.717][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.723][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.730][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.736][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.738][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.739][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.740][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.742][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:56.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.780][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.783][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.785][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.786][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:56.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.803][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.809][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.814][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.820][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.822][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.823][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.824][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.826][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:56.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.860][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.861][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.863][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.864][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:56.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.882][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.889][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.895][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.901][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.902][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.903][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.905][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.906][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:56.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.937][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.938][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.939][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.940][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:56.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:56.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.957][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.962][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.967][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.973][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.974][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.975][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.976][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.978][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:56.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:56.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:56.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:56.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:56.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:57.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.003][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:57.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:57.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.008][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:57.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:57.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.013][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:57.014][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:57.016][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.017][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:57.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:57.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.034][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.040][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.045][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.050][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.051][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.053][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.054][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.055][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.086][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.088][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.089][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.090][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.106][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.125][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.127][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.129][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.131][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.132][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.173][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.175][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.176][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.177][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.178][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.196][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.203][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.210][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.220][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.222][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.224][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.226][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.228][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.255][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:57.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:57.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.265][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:57.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:57.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.271][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:57.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:57.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.276][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:57.277][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:57.278][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.280][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.281][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:57.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:57.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:57.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:57.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.303][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:57.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:57.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:57.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:57.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.320][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:57.322][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:57.323][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.324][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:57.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:57.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.375][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.376][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.378][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.380][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.408][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.418][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.426][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.436][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.438][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.441][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.443][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.445][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.467][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:57.469][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:57.470][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.471][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.478][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.479][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-24 16:02:57.480][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.482][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.488][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.490][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-24 16:02:57.491][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.492][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.499][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-24 16:02:57.500][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-24 16:02:57.501][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.503][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.509][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:57.511][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-24 16:02:57.512][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.513][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.519][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.521][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:57.522][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.523][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.530][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.531][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:57.533][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.534][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.540][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.542][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-24 16:02:57.543][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.544][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.556][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:57.557][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:57.558][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.560][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.566][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:57.567][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:57.569][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.570][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.576][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:57.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:57.579][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.580][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.586][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.588][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:57.589][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.590][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.596][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:57.598][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-24 16:02:57.599][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.600][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.607][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.608][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:57.610][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.611][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.617][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:57.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:57.620][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.621][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.628][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:57.629][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:57.630][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.631][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.638][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:57.639][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:57.641][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.642][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:57.648][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-24 16:02:57.650][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-24 16:02:57.651][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.652][ef$get] fields variable is a list.
biodb.INFO [2026-01-24 16:02:57.663][biodb::testThat]
biodb.INFO [2026-01-24 16:02:57.664][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-24 16:02:57.666][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:57.667][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:57.686][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-24 16:02:57.690][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-24 16:02:57.694][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-24 16:02:57.734][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-24 16:02:57.736][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-24 16:02:57.737][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-24 16:02:57.914][biodb::testThat]
biodb.INFO [2026-01-24 16:02:57.917][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-24 16:02:57.919][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:57.922][biodb::testThat]
biodb.TRACE[2026-01-24 16:02:57.926][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:57.929][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:57.931][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:57.932][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:57.936][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-01-24 16:02:57.980][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-24 16:02:58.061][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-24 16:02:58.063][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-24 16:02:58.064][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-24 16:02:58.066][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-24 16:02:58.087][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-24 16:02:58.159][biodb::testThat]
biodb.INFO [2026-01-24 16:02:58.161][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-24 16:02:58.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:58.163][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:58.173][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-24 16:02:58.174][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-24 16:02:58.176][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-24 16:02:58.178][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-24 16:02:58.179][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-24 16:02:58.180][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-24 16:02:58.241][biodb::testThat]
biodb.INFO [2026-01-24 16:02:58.242][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-24 16:02:58.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:58.245][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:58.250][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-24 16:02:58.251][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-24 16:02:58.253][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-24 16:02:58.254][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-24 16:02:58.256][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-24 16:02:58.257][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-24 16:02:58.313][biodb::testThat]
biodb.INFO [2026-01-24 16:02:58.315][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-24 16:02:58.316][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:58.317][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-24 16:02:58.419][biodb::testThat]
biodb.INFO [2026-01-24 16:02:58.420][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-24 16:02:58.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:58.423][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-24 16:02:58.481][biodb::testThat]
biodb.INFO [2026-01-24 16:02:58.483][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:58.484][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:58.485][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-24 16:02:58.544][biodb::testThat]
biodb.INFO [2026-01-24 16:02:58.545][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:58.546][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:58.548][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-01-24 16:02:58.631][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:58.632][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:58.634][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:58.635][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:58.636][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:58.637][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:58.638][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:58.640][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:58.641][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:58.642][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:58.643][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:58.645][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:58.646][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:58.647][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:58.648][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:58.650][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:58.651][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:58.652][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:58.653][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:58.654][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:58.656][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:58.657][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-24 16:02:58.658][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:58.659][ef$get] fields variable is a list.
biodb.INFO [2026-01-24 16:02:58.661][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-24 16:02:58.662][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-01-24 16:02:58.663][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-24 16:02:58.664][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:58.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:58.667][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:58.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:58.669][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:58.670][FUN] Functions in observer 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)