Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-13 23:55 -0500 (Sat, 13 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4882
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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

CHECK results for biodbHmdb on nebbiolo2

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-12-13 16:01:09 -0500 (Sat, 13 Dec 2025)
EndedAt: 2025-12-13 16:02:18 -0500 (Sat, 13 Dec 2025)
EllapsedTime: 69.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-12-13 16:02:14.752][biodb::testContext]
biodb.INFO [2025-12-13 16:02:14.754][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:02:14.755][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-13 16:02:14.756][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:02:14.757][biodb::testContext]
biodb.INFO [2025-12-13 16:02:14.763][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:02:14.765][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:02:14.772][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:02:14.773][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:02:14.774][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:02:14.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.777][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:02:14.794][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:02:14.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.798][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:02:14.799][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:02:14.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.811][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:02:14.812][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:02:14.813][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:02:14.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.816][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:02:14.817][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:02:14.818][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:02:14.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.822][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:02:14.823][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:02:14.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.826][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:02:14.827][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:02:14.828][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:02:14.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.831][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:02:14.832][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:02:14.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.836][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:02:14.837][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:02:14.838][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:02:14.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.841][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:02:14.842][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:02:14.843][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:02:14.844][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:02:14.845][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:02:14.846][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:02:14.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.849][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:02:14.850][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:02:14.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.853][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:02:14.854][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:02:14.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.858][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:02:14.859][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:02:14.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.862][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:02:14.863][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:02:14.864][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:02:14.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.868][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:02:14.869][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:02:14.873][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:02:14.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.876][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:02:14.877][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:02:14.878][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:02:14.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:14.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:14.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:14.884][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:02:14.914][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:14.929][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-13 16:02:14.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:14.932][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:14.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:14.935][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:14.936][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:02:14.937][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:14.938][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.939][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:02:14.940][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:14.941][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:14.941][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.942][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:02:14.942][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:02:14.942][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:02:14.942][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:02:14.942][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:02:14.943][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:02:14.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:14.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:14.946][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:14.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:14.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:14.949][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:14.950][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:14.950][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:14.951][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:14.952][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:14.953][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:14.954][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:02:14.956][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:14.957][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:02:14.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:14.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:14.961][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:14.967][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:14.968][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:02:14.969][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:14.970][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.970][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:02:14.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:14.972][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:14.973][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.974][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:02:14.974][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:02:14.974][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:02:14.974][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:02:14.974][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:02:14.975][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:02:14.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:14.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:14.978][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:14.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:14.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:14.980][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:14.981][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:14.982][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:14.983][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:14.984][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:14.985][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:14.986][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:02:14.988][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.989][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-13 16:02:14.990][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.991][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:14.992][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:14.992][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:14.993][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:14.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:14.995][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:02:14.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:14.997][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:14.998][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:02:14.999][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:15.000][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.001][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.002][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.003][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:02:15.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:15.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:15.005][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:15.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:15.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:15.008][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:15.009][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.010][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:15.011][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:15.012][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:15.012][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.014][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:02:15.015][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.016][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:02:15.017][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.018][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:15.019][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.020][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:02:15.021][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:15.022][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:15.023][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:02:15.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:15.025][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:15.026][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:02:15.027][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:15.027][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.028][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.029][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.030][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:02:15.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:15.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:15.033][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:15.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:15.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:15.036][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:15.036][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:15.038][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:15.039][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:15.040][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.044][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:02:15.044][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.066][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[2025-12-13 16:02:15.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.079][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[2025-12-13 16:02:15.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.112][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[2025-12-13 16:02:15.113][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:02:15.118][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:02:15.119][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:02:15.120][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:02:15.122][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:02:15.127][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:02:15.129][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:02:15.130][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:02:15.131][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:02:15.132][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:02:15.134][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:02:15.135][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:02:15.136][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:02:15.138][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:02:15.139][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:02:15.140][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:02:15.141][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:02:15.143][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:02:15.144][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:02:15.145][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:02:15.147][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:02:15.148][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:02:15.149][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:02:15.151][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:02:15.155][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:02:15.158][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:02:15.160][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:02:15.162][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:02:15.163][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:02:15.165][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:02:15.166][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:02:15.168][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:02:15.169][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:02:15.171][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:02:15.172][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:02:15.174][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:02:15.175][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:02:15.177][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:02:15.178][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:02:15.180][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:02:15.181][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:02:15.182][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:02:15.184][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:02:15.185][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:02:15.187][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:02:15.188][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:02:15.190][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:02:15.191][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:02:15.193][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:02:15.194][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:02:15.196][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:02:15.197][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:02:15.199][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:02:15.200][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:02:15.201][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:02:15.203][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:02:15.204][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:02:15.206][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:02:15.207][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:02:15.209][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:02:15.210][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:02:15.212][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:02:15.213][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:02:15.215][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:02:15.216][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:02:15.217][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:02:15.219][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:02:15.220][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:02:15.222][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:02:15.223][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:02:15.225][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:02:15.226][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:02:15.228][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:02:15.229][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:02:15.230][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:02:15.232][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:02:15.233][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:02:15.235][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:02:15.236][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:02:15.238][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:02:15.239][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:02:15.241][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:02:15.242][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:02:15.249][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:02:15.251][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:02:15.255][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:02:15.256][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.258][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-12-13 16:02:15.374][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-12-13 16:02:15.382][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-12-13 16:02:15.395][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-12-13 16:02:15.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:02:15.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:02:15.403][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-12-13 16:02:15.411][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-12-13 16:02:15.413][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:15.414][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-12-13 16:02:15.415][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.416][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:02:15.417][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:15.418][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-12-13 16:02:15.419][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:02:15.420][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-13 16:02:15.421][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:02:15.422][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.423][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-12-13 16:02:15.424][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-12-13 16:02:15.425][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-12-13 16:02:15.426][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:02:15.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:02:15.427][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-12-13 16:02:15.427][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-12-13 16:02:15.428][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:02:15.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:15.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:15.431][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:02:15.432][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:02:15.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:02:15.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:02:15.434][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-12-13 16:02:15.434][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-12-13 16:02:15.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:02:15.436][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:02:15.437][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:02:15.438][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:02:15.443][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-12-13 16:02:15.445][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:02:15.446][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:02:15.448][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:02:15.449][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:02:15.473][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-12-13 16:02:15.488][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-12-13 16:02:15.495][biodb::testThat]
biodb.INFO [2025-12-13 16:02:15.496][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-13 16:02:15.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:15.498][biodb::testThat]
biodb.TRACE[2025-12-13 16:02:15.501][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-12-13 16:02:15.503][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:02:15.506][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-12-13 16:02:15.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:02:15.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:15.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:15.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:15.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:15.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:15.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:02:15.540][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:15.541][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:15.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.543][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:15.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:15.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.559][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.560][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.562][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.586][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.590][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.591][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.593][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.594][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.598][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.599][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.601][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.602][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.606][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.607][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.609][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.614][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.615][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.616][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.630][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.631][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.633][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.634][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.638][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.639][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.641][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.642][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.646][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.647][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.648][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.653][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.654][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.656][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.661][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:15.662][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:15.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.664][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:15.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.669][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:15.670][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:15.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.672][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:15.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:15.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.677][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.678][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.679][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.684][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.685][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.687][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.692][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:15.693][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:15.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.695][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:15.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:15.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.700][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:15.701][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:15.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.702][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.703][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:15.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:15.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.707][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:15.708][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:15.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.710][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:15.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:15.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.715][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-12-13 16:02:15.716][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:15.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.718][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.719][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-12-13 16:02:15.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:15.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:15.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:15.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:15.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:15.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:15.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:15.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.806][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.810][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.814][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:15.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.818][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.822][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.825][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:15.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:15.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:15.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.851][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.859][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:15.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.862][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:15.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:15.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:15.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:15.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:15.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.881][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:15.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:15.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.885][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:15.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:15.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.888][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:15.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:15.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.892][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:15.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:15.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.896][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:15.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:15.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.899][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:15.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:15.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.907][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:15.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:15.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:15.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:15.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:15.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:15.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.918][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:15.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:15.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:15.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.933][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.936][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.940][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:15.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:15.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:15.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:15.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:15.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:15.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:15.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:15.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.970][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.974][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:15.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.977][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.981][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.985][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:15.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.988][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:15.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:15.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.992][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:15.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:15.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:15.996][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:15.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:15.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:15.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.000][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-13 16:02:16.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.014][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-13 16:02:16.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.057][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.061][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.068][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:02:16.094][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-12-13 16:02:16.096][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:02:16.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:02:16.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.100][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:02:16.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:02:16.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.104][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:02:16.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:02:16.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.108][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:02:16.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:02:16.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.120][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.155][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.159][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.162][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-13 16:02:16.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.183][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.184][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.186][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.197][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.201][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.205][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.209][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.210][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.211][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.212][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.234][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.235][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.236][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.248][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.251][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.255][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.259][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.260][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.262][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.263][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.289][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.290][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.291][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.303][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.306][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.310][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.314][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.315][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.317][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.318][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.339][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.340][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.342][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.353][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:16.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:16.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.357][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:16.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:16.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.361][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:16.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:16.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.364][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:16.365][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:16.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.367][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.368][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:16.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:16.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.378][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:16.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:16.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:16.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:16.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:16.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:16.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.393][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:16.394][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:16.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.396][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:16.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:16.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.407][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.411][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.415][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.418][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.419][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.421][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.422][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.444][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.445][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.446][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.462][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.469][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.470][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.472][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.494][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.495][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.497][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.517][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.524][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.525][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.527][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.538][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:16.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:16.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.542][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.546][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:16.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:16.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.550][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:16.551][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:16.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.552][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.553][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:16.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:16.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:16.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:16.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:16.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:16.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:16.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:16.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.575][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:16.576][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:16.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.578][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:16.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:16.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.600][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.601][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.603][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.614][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.618][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.621][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.629][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.630][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.632][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.633][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.643][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:02:16.644][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:02:16.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.646][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.650][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.651][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-13 16:02:16.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.653][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.656][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.657][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:02:16.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.659][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.663][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.664][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-13 16:02:16.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.666][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.670][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.671][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-13 16:02:16.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.673][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.676][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.677][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-13 16:02:16.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.679][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.683][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.684][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-13 16:02:16.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.686][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.690][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.691][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-13 16:02:16.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.692][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.696][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:16.697][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:16.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.699][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.703][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:02:16.704][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:02:16.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.705][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:02:16.710][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:02:16.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.712][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.716][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.717][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:02:16.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.719][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.722][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.723][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-13 16:02:16.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.725][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.729][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.730][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-13 16:02:16.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.732][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.735][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.736][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.738][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.746][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.747][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-13 16:02:16.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.749][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.753][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.754][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:16.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.755][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:16.759][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-13 16:02:16.760][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-13 16:02:16.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.762][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:02:16.768][biodb::testThat]
biodb.INFO [2025-12-13 16:02:16.769][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-13 16:02:16.770][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:16.771][biodb::testThat]
biodb.DEBUG[2025-12-13 16:02:16.784][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-13 16:02:16.786][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-13 16:02:16.789][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-13 16:02:16.816][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-13 16:02:16.818][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-13 16:02:16.819][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-13 16:02:16.942][biodb::testThat]
biodb.INFO [2025-12-13 16:02:16.943][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-13 16:02:16.944][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:16.945][biodb::testThat]
biodb.TRACE[2025-12-13 16:02:16.948][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:16.954][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:16.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:16.956][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:02:16.957][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-12-13 16:02:16.976][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-13 16:02:17.019][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-13 16:02:17.020][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-13 16:02:17.021][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-13 16:02:17.023][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-13 16:02:17.034][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-13 16:02:17.087][biodb::testThat]
biodb.INFO [2025-12-13 16:02:17.088][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-13 16:02:17.089][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:17.090][biodb::testThat]
biodb.DEBUG[2025-12-13 16:02:17.096][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-13 16:02:17.097][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-13 16:02:17.099][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-13 16:02:17.100][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-13 16:02:17.101][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-13 16:02:17.102][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-13 16:02:17.144][biodb::testThat]
biodb.INFO [2025-12-13 16:02:17.145][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-13 16:02:17.146][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:17.147][biodb::testThat]
biodb.DEBUG[2025-12-13 16:02:17.150][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-13 16:02:17.151][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-13 16:02:17.152][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-13 16:02:17.154][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-13 16:02:17.155][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-13 16:02:17.156][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-13 16:02:17.194][biodb::testThat]
biodb.INFO [2025-12-13 16:02:17.195][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-13 16:02:17.196][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:17.197][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-13 16:02:17.240][biodb::testThat]
biodb.INFO [2025-12-13 16:02:17.241][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-13 16:02:17.242][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:17.242][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-13 16:02:17.282][biodb::testThat]
biodb.INFO [2025-12-13 16:02:17.283][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-13 16:02:17.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:17.285][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-13 16:02:17.329][biodb::testThat]
biodb.INFO [2025-12-13 16:02:17.330][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-13 16:02:17.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:02:17.332][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-12-13 16:02:17.384][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:17.385][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:17.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:17.387][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:17.388][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:17.389][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:17.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:17.391][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:17.392][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:17.393][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:17.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:17.395][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:17.396][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:02:17.397][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:02:17.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:17.398][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:17.399][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-13 16:02:17.400][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-13 16:02:17.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:17.402][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:02:17.403][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:17.404][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-13 16:02:17.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:02:17.406][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:02:17.407][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:02:17.408][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-12-13 16:02:17.409][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:02:17.413][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:02:17.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:02:17.415][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:02:17.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:02:17.417][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:02:17.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/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)