Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-25 23:55 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-25 09:55 -0400 (Sat, 25 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: fa89c02
git_last_commit_date: 2025-07-24 10:45:35 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on lconway

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

raw results


Summary

Package: biodbHmdb
Version: 1.15.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.1.tar.gz
StartedAt: 2025-10-25 16:01:21 -0400 (Sat, 25 Oct 2025)
EndedAt: 2025-10-25 16:02:23 -0400 (Sat, 25 Oct 2025)
EllapsedTime: 62.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-10-25 16:02:20.622][biodb::testContext]
biodb.INFO [2025-10-25 16:02:20.625][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:02:20.626][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-25 16:02:20.626][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:02:20.627][biodb::testContext]
biodb.INFO [2025-10-25 16:02:20.632][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:02:20.633][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-25 16:02:20.639][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:20.640][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-25 16:02:20.640][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-25 16:02:20.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.643][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-25 16:02:20.657][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-25 16:02:20.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.660][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-25 16:02:20.661][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-25 16:02:20.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.672][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-25 16:02:20.673][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-25 16:02:20.674][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-25 16:02:20.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.676][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-25 16:02:20.677][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-25 16:02:20.678][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-25 16:02:20.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.681][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-25 16:02:20.681][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-25 16:02:20.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.684][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-25 16:02:20.685][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-25 16:02:20.686][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-25 16:02:20.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.688][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-25 16:02:20.689][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-25 16:02:20.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.692][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-25 16:02:20.693][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-25 16:02:20.694][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-25 16:02:20.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.697][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:02:20.697][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-25 16:02:20.698][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-25 16:02:20.699][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-25 16:02:20.700][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-25 16:02:20.701][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-25 16:02:20.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.703][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-25 16:02:20.704][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-25 16:02:20.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.707][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-25 16:02:20.708][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-25 16:02:20.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.711][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-25 16:02:20.712][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-25 16:02:20.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.715][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-25 16:02:20.715][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-25 16:02:20.716][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-25 16:02:20.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.719][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:02:20.720][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-25 16:02:20.742][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-25 16:02:20.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.746][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-25 16:02:20.746][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-25 16:02:20.747][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-25 16:02:20.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.752][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-25 16:02:20.778][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.791][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-25 16:02:20.792][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:20.794][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.796][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.797][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.798][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:02:20.799][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:20.800][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.801][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-25 16:02:20.801][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:20.802][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.803][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.804][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:02:20.804][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:02:20.804][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:02:20.804][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:02:20.804][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:02:20.805][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:20.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:20.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:20.808][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:20.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:20.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:20.810][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.811][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.812][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:20.813][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:20.813][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.814][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.815][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-25 16:02:20.817][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.818][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:02:20.818][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.819][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:20.825][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.826][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.826][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.827][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.828][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:02:20.829][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:20.830][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.831][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-25 16:02:20.831][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:20.832][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.833][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.834][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:02:20.834][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:02:20.834][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:02:20.834][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:02:20.834][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:02:20.835][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:20.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:20.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:20.837][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:20.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:20.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:20.839][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.840][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.841][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:20.842][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:20.843][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.844][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.845][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-25 16:02:20.846][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.847][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-25 16:02:20.848][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.849][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:20.850][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.851][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.851][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.852][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.853][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:02:20.854][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:20.855][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.856][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-25 16:02:20.857][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:20.857][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.858][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.859][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.860][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:20.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:20.861][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:20.862][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:20.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:20.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:20.865][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.865][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.866][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:20.867][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:20.868][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.868][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.869][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-25 16:02:20.871][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.872][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:02:20.872][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.873][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:20.874][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.875][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.876][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.876][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.877][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:02:20.878][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:20.879][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.880][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-25 16:02:20.881][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:20.881][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.882][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:20.883][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.884][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:20.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:20.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:20.886][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:20.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:20.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:20.888][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:20.889][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.890][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:20.891][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:20.891][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:20.892][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:20.895][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:20.896][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.910][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[2025-10-25 16:02:20.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.922][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[2025-10-25 16:02:20.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.952][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[2025-10-25 16:02:20.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:20.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:20.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:20.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:20.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:20.956][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-25 16:02:20.964][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-25 16:02:20.965][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-25 16:02:20.966][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-25 16:02:20.967][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-25 16:02:20.969][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-25 16:02:20.970][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-25 16:02:20.971][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-25 16:02:20.972][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-25 16:02:20.973][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-25 16:02:20.974][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-25 16:02:20.975][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-25 16:02:20.977][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-25 16:02:20.978][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-25 16:02:20.979][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-25 16:02:20.980][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-25 16:02:20.981][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-25 16:02:20.982][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-25 16:02:20.984][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-25 16:02:20.985][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-25 16:02:20.986][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-25 16:02:20.987][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-25 16:02:20.988][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-25 16:02:20.990][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-25 16:02:20.991][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-25 16:02:20.992][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-25 16:02:20.993][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-25 16:02:20.994][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-25 16:02:20.995][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-25 16:02:20.996][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-25 16:02:20.998][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-25 16:02:20.999][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-25 16:02:21.000][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-25 16:02:21.001][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-25 16:02:21.002][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-25 16:02:21.003][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-25 16:02:21.004][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-25 16:02:21.006][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-25 16:02:21.007][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-25 16:02:21.008][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-25 16:02:21.009][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-25 16:02:21.010][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-25 16:02:21.011][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-25 16:02:21.013][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-25 16:02:21.014][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-25 16:02:21.015][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-25 16:02:21.016][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-25 16:02:21.017][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-25 16:02:21.018][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-25 16:02:21.019][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-25 16:02:21.020][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-25 16:02:21.021][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-25 16:02:21.023][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-25 16:02:21.024][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-25 16:02:21.025][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-25 16:02:21.026][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-25 16:02:21.027][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-25 16:02:21.028][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-25 16:02:21.030][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-25 16:02:21.031][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-25 16:02:21.032][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-25 16:02:21.033][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-25 16:02:21.034][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-25 16:02:21.035][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-25 16:02:21.036][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-25 16:02:21.038][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-25 16:02:21.039][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-25 16:02:21.040][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-25 16:02:21.041][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-25 16:02:21.042][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-25 16:02:21.043][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-25 16:02:21.044][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-25 16:02:21.045][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-25 16:02:21.046][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-25 16:02:21.047][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-25 16:02:21.048][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-25 16:02:21.049][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-25 16:02:21.050][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-25 16:02:21.052][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-25 16:02:21.053][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-25 16:02:21.054][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-25 16:02:21.055][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-25 16:02:21.056][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-25 16:02:21.060][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-25 16:02:21.061][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:02:21.063][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:21.064][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.065][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-10-25 16:02:21.152][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-10-25 16:02:21.159][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-10-25 16:02:21.169][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-10-25 16:02:21.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:21.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:21.175][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-10-25 16:02:21.182][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-10-25 16:02:21.183][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:21.184][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-10-25 16:02:21.185][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:21.186][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:21.186][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:21.187][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-10-25 16:02:21.188][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:21.188][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:21.189][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-25 16:02:21.190][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:21.191][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:21.191][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-10-25 16:02:21.192][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-10-25 16:02:21.193][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-10-25 16:02:21.194][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:21.195][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:02:21.195][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-10-25 16:02:21.195][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-10-25 16:02:21.195][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-25 16:02:21.196][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:21.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:21.198][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:21.198][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:21.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:21.200][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:21.201][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-10-25 16:02:21.201][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-10-25 16:02:21.201][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:21.202][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:21.203][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:21.203][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:21.212][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-10-25 16:02:21.213][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-25 16:02:21.214][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-25 16:02:21.215][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-25 16:02:21.216][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-25 16:02:21.233][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-10-25 16:02:21.245][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-10-25 16:02:21.251][biodb::testThat]
biodb.INFO [2025-10-25 16:02:21.252][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-25 16:02:21.253][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:21.254][biodb::testThat]
biodb.TRACE[2025-10-25 16:02:21.257][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-10-25 16:02:21.259][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-10-25 16:02:21.261][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-10-25 16:02:21.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-25 16:02:21.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:21.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:21.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:21.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:21.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:21.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-25 16:02:21.290][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.291][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.292][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.306][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.307][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.308][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.327][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.331][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.332][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.333][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.335][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.338][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.339][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.340][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.342][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.345][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.355][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.357][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.361][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.362][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.364][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.369][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.370][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.372][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.373][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.376][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.377][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.379][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.380][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.383][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.384][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.386][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.387][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.391][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.392][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.393][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.398][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:21.399][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:21.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.400][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.401][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:21.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:21.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.405][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:21.406][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:21.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.408][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:21.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:21.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.412][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.413][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.414][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.419][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.420][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.421][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.426][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.428][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.433][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:21.434][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:21.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.435][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.436][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:21.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:21.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.440][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:21.441][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:21.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.442][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.443][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:21.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:21.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.447][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-10-25 16:02:21.447][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:21.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.449][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.450][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-10-25 16:02:21.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:21.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.530][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.533][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.536][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:21.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.539][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.542][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.545][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:21.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.565][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.567][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:21.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.573][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.576][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.579][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:21.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.582][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:21.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:21.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:21.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:21.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.588][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:21.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:21.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.594][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:21.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:21.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.597][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:21.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:21.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.600][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:21.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:21.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.603][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:21.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:21.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.606][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:21.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:21.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.609][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:21.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:21.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:21.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:21.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:21.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:21.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:21.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:21.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.629][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.632][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.635][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:21.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.655][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.658][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.661][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.663][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.667][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.669][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.673][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:21.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:21.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.676][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:21.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:21.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.679][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:21.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:21.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.682][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-25 16:02:21.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.700][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-25 16:02:21.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:21.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.738][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.741][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.748][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-25 16:02:21.772][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-10-25 16:02:21.775][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:02:21.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:02:21.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.778][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:02:21.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:02:21.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.781][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-25 16:02:21.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-25 16:02:21.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.785][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-25 16:02:21.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-25 16:02:21.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.801][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.834][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.837][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-25 16:02:21.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.855][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.856][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.858][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:21.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:21.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.868][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.872][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.875][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.878][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.879][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.880][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.881][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:21.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.900][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.901][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.903][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:21.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.918][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.921][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.924][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.927][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.928][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.929][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.930][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:21.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.948][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.949][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.950][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:21.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.961][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.964][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.967][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.970][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.971][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.972][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.973][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:21.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.991][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.992][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.993][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:21.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:21.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:21.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:21.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.004][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:22.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:22.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.010][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:22.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:22.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.013][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:22.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:22.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.016][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:22.017][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:22.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.018][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.019][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:22.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:22.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.029][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:22.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:22.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:22.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:22.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:22.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:22.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.038][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:22.038][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:22.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.040][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:22.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:22.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.050][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.053][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.056][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.059][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.060][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.061][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.062][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.081][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.083][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.096][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.099][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.102][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.103][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.104][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.105][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.125][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.128][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.129][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.130][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.131][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.141][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.144][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.150][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.151][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.152][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.153][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.163][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:22.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:22.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.166][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:22.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:22.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.169][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:22.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:22.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.172][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:22.172][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:22.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.174][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.175][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:22.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:22.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:22.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:22.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:22.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:22.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:22.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:22.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.194][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:22.195][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:22.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.196][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:22.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:22.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.220][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.221][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.223][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.233][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.236][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.239][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.242][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.243][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.244][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.245][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.255][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:22.256][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:22.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.257][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.262][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.263][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-25 16:02:22.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.264][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.269][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.270][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:22.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.271][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.276][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-25 16:02:22.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-25 16:02:22.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.278][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.282][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:22.283][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-25 16:02:22.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.285][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.289][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.290][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-25 16:02:22.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.291][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.296][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.296][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-25 16:02:22.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.298][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.302][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.303][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-25 16:02:22.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.304][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.308][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:22.309][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:22.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.310][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.315][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:22.315][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:22.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.317][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.321][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:22.322][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:22.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.327][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.331][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.332][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:22.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.333][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.337][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:22.338][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-25 16:02:22.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.339][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.344][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.344][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-25 16:02:22.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.346][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.350][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:22.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:22.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.352][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.357][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:22.357][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-25 16:02:22.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.359][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.363][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:22.364][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:22.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.366][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.370][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-25 16:02:22.370][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-25 16:02:22.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.372][ef$get] fields variable is a list.
biodb.INFO [2025-10-25 16:02:22.379][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.379][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-25 16:02:22.380][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:22.381][biodb::testThat]
biodb.DEBUG[2025-10-25 16:02:22.390][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-25 16:02:22.394][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-25 16:02:22.396][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-25 16:02:22.416][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-25 16:02:22.417][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-25 16:02:22.418][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-25 16:02:22.450][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.451][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-25 16:02:22.452][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:22.453][biodb::testThat]
biodb.TRACE[2025-10-25 16:02:22.455][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:22.456][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:22.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.458][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-25 16:02:22.459][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-10-25 16:02:22.476][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-25 16:02:22.511][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-25 16:02:22.513][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-25 16:02:22.514][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-25 16:02:22.515][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-25 16:02:22.523][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-25 16:02:22.541][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.542][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-25 16:02:22.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:22.544][biodb::testThat]
biodb.DEBUG[2025-10-25 16:02:22.550][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-25 16:02:22.551][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-25 16:02:22.552][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-25 16:02:22.553][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-25 16:02:22.554][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-25 16:02:22.554][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-25 16:02:22.565][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.566][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-25 16:02:22.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:22.567][biodb::testThat]
biodb.DEBUG[2025-10-25 16:02:22.570][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-25 16:02:22.571][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-25 16:02:22.572][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-25 16:02:22.573][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-25 16:02:22.574][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-25 16:02:22.574][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-25 16:02:22.585][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.586][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-25 16:02:22.587][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:22.588][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.602][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.603][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-25 16:02:22.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:22.605][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.615][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.616][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-25 16:02:22.617][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:22.618][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.629][biodb::testThat]
biodb.INFO [2025-10-25 16:02:22.629][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-25 16:02:22.630][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:22.631][biodb::testThat]
biodb.TRACE[2025-10-25 16:02:22.650][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:22.651][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:22.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.653][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.653][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:22.654][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:22.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.655][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.656][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:22.657][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:22.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.658][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.659][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:22.660][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:22.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.661][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.662][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-25 16:02:22.663][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-25 16:02:22.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.664][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:22.665][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:22.665][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-25 16:02:22.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:22.667][ef$get] fields variable is a list.
biodb.INFO [2025-10-25 16:02:22.667][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-25 16:02:22.668][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-10-25 16:02:22.669][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-25 16:02:22.670][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:22.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:22.671][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:22.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:22.672][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:22.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]

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

[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.15.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.15.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)