Back to Long Tests report for BioC 3.22

This page was generated on 2025-08-09 23:55 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/29HostnameOS / ArchCHECK
biodbHmdb 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-09 09:55 -0400 (Sat, 09 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: fa89c02
git_last_commit_date: 2025-07-24 10:45:35 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on palomino8

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

raw results


Summary

Package: biodbHmdb
Version: 1.15.1
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.1.tar.gz
StartedAt: 2025-08-09 16:02:49 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 16:04:30 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 100.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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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 [2025-08-09 16:04:26.827][biodb::testContext]
biodb.INFO [2025-08-09 16:04:26.830][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:04:26.831][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-09 16:04:26.832][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:04:26.833][biodb::testContext]
biodb.INFO [2025-08-09 16:04:26.839][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:04:26.842][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-09 16:04:26.850][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:04:26.851][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-09 16:04:26.853][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-09 16:04:26.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.857][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-09 16:04:26.873][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-09 16:04:26.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.876][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:26.877][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-09 16:04:26.879][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-09 16:04:26.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.883][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-09 16:04:26.885][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-09 16:04:26.886][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-09 16:04:26.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.889][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:26.890][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-09 16:04:26.891][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-09 16:04:26.893][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-09 16:04:26.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.897][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-09 16:04:26.898][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-09 16:04:26.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.902][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:26.903][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-09 16:04:26.904][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-09 16:04:26.905][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-09 16:04:26.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.910][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-09 16:04:26.911][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-09 16:04:26.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.915][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-09 16:04:26.916][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-09 16:04:26.918][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-09 16:04:26.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.922][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:04:26.923][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-09 16:04:26.925][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-09 16:04:26.926][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-09 16:04:26.927][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-09 16:04:26.928][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-09 16:04:26.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.931][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:26.933][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-09 16:04:26.934][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-09 16:04:26.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.938][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-09 16:04:26.940][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-09 16:04:26.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.950][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-09 16:04:26.951][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-09 16:04:26.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.955][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-09 16:04:26.956][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-09 16:04:26.958][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-09 16:04:26.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.961][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:26.962][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:04:26.963][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-09 16:04:26.967][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-09 16:04:26.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.971][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-09 16:04:26.973][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-09 16:04:26.974][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-09 16:04:26.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:26.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:26.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:26.980][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-09 16:04:27.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.021][self$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[2025-08-09 16:04:27.022][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.023][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:04:27.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.026][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.027][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.028][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.029][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:04:27.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:04:27.032][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.033][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-09 16:04:27.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:04:27.035][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.037][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.038][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:04:27.038][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:04:27.038][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:04:27.038][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:04:27.038][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:04:27.039][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:04:27.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:04:27.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.046][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.047][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.048][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:04:27.049][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:04:27.050][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.052][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.053][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-09 16:04:27.055][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.056][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:04:27.057][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:04:27.060][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.064][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:04:27.066][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:04:27.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.068][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-09 16:04:27.069][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:04:27.070][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.072][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.073][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:04:27.073][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:04:27.073][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:04:27.073][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:04:27.073][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:04:27.074][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:04:27.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.078][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:04:27.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.081][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.082][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:04:27.084][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:04:27.086][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.087][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.088][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-09 16:04:27.090][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.091][self$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[2025-08-09 16:04:27.093][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.094][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:04:27.095][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.097][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.098][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.100][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:04:27.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:04:27.102][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.103][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-09 16:04:27.105][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:04:27.106][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.107][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.108][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.109][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:04:27.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.113][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:04:27.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.117][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:04:27.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:04:27.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.122][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.123][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-09 16:04:27.125][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.127][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:04:27.133][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.134][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:04:27.135][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.137][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.138][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.139][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.140][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:04:27.141][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:04:27.143][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.144][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-09 16:04:27.145][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:04:27.146][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.147][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.149][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.150][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:04:27.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.153][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:04:27.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.155][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.157][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.158][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:04:27.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:04:27.161][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.162][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.166][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:04:27.167][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.168][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.179][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.184][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.195][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.200][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.206][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.217][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.227][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.238][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.244][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.249][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.256][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-09 16:04:27.260][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-09 16:04:27.261][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-09 16:04:27.263][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-09 16:04:27.264][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-09 16:04:27.266][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-09 16:04:27.267][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-09 16:04:27.269][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-09 16:04:27.270][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-09 16:04:27.272][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-09 16:04:27.274][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-09 16:04:27.275][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-09 16:04:27.277][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-09 16:04:27.278][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-09 16:04:27.280][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:04:27.281][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:04:27.283][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-09 16:04:27.284][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-09 16:04:27.286][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-09 16:04:27.287][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-09 16:04:27.289][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-09 16:04:27.290][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-09 16:04:27.292][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-09 16:04:27.294][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-09 16:04:27.295][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-09 16:04:27.297][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-09 16:04:27.298][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-09 16:04:27.300][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-09 16:04:27.301][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-09 16:04:27.303][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-09 16:04:27.304][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-09 16:04:27.306][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-09 16:04:27.308][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-09 16:04:27.309][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-09 16:04:27.311][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-09 16:04:27.312][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-09 16:04:27.314][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-09 16:04:27.315][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-09 16:04:27.317][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-09 16:04:27.318][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-09 16:04:27.320][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-09 16:04:27.322][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-09 16:04:27.323][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-09 16:04:27.325][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-09 16:04:27.332][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-09 16:04:27.333][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:04:27.335][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-09 16:04:27.337][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-09 16:04:27.338][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-09 16:04:27.340][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-09 16:04:27.341][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-09 16:04:27.343][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-09 16:04:27.344][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-09 16:04:27.346][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-09 16:04:27.347][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-09 16:04:27.349][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-09 16:04:27.350][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-09 16:04:27.352][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-09 16:04:27.354][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-09 16:04:27.355][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-09 16:04:27.357][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-09 16:04:27.358][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-09 16:04:27.360][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-09 16:04:27.361][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-09 16:04:27.363][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-09 16:04:27.364][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-09 16:04:27.366][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-09 16:04:27.368][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-09 16:04:27.369][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-09 16:04:27.371][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-09 16:04:27.372][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-09 16:04:27.374][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-09 16:04:27.375][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-09 16:04:27.377][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-09 16:04:27.378][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-09 16:04:27.380][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-09 16:04:27.381][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-09 16:04:27.383][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-09 16:04:27.385][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-09 16:04:27.386][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-09 16:04:27.388][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-09 16:04:27.389][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-09 16:04:27.391][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-09 16:04:27.425][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-09 16:04:27.428][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:04:27.431][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:04:27.432][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.434][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.435][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.446][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.454][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.469][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.476][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.484][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.491][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.499][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.507][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.514][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.522][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.537][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:04:27.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-08-09 16:04:27.566][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-08-09 16:04:27.574][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-08-09 16:04:27.586][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-09 16:04:27.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:04:27.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.594][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.597][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-08-09 16:04:27.606][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-08-09 16:04:27.608][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.609][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.610][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.611][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:04:27.613][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.614][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-08-09 16:04:27.615][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.617][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-09 16:04:27.619][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:04:27.620][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.621][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-08-09 16:04:27.622][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-08-09 16:04:27.623][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-08-09 16:04:27.625][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:04:27.626][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:04:27.626][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-08-09 16:04:27.626][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-08-09 16:04:27.627][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:04:27.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.631][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:04:27.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:04:27.633][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:04:27.634][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:04:27.635][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-08-09 16:04:27.635][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-08-09 16:04:27.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:04:27.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:04:27.639][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:04:27.640][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:04:27.645][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-08-09 16:04:27.647][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-09 16:04:27.649][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-09 16:04:27.650][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-09 16:04:27.652][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:04:27.672][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-08-09 16:04:27.698][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-08-09 16:04:27.707][biodb::testThat]
biodb.INFO [2025-08-09 16:04:27.709][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-09 16:04:27.710][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:27.711][biodb::testThat]
biodb.TRACE[2025-08-09 16:04:27.717][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-08-09 16:04:27.719][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:04:27.723][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-08-09 16:04:27.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:04:27.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:27.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:27.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:27.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:27.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:27.761][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:04:27.770][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:27.772][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:27.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.774][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:27.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:27.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.792][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:27.793][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:27.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.795][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.817][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:27.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:27.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.823][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:27.824][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:27.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.826][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.828][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:27.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:27.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.833][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:27.834][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:27.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.837][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.838][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:27.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:27.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.843][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:27.844][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:27.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.847][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:27.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:27.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.853][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:27.855][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:27.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.857][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:27.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:27.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.863][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:27.865][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:27.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.867][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.869][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:27.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:27.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.874][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:27.875][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:27.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.877][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.879][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:27.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:27.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.884][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:27.885][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:27.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.888][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:27.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:27.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.894][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:27.895][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:27.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.898][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.899][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:27.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:27.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.910][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:27.911][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:27.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.914][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.915][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:27.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:27.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.920][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:27.921][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:27.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.924][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:27.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:27.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.930][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:27.932][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:27.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.934][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:27.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:27.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.941][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:27.942][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:27.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.944][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:27.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:27.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.951][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:27.952][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:27.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.954][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:27.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:27.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.961][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:27.962][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:27.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.966][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.968][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:27.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:27.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.973][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:27.974][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:27.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.977][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.978][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:27.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:27.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.983][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-08-09 16:04:27.985][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:27.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.987][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.989][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-08-09 16:04:27.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:27.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:27.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:27.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:27.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:27.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.036][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.041][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.050][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.055][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:28.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.060][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:28.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:28.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.065][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:28.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.100][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.105][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.110][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.115][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:28.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:28.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.120][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:28.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:28.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.125][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:28.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:28.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.129][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.139][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.144][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:28.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:28.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.149][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:28.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:28.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.154][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:28.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:28.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.159][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:28.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:28.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:28.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:28.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.169][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:28.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:28.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:28.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:28.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:28.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:28.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:28.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:28.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.198][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.203][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.246][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.251][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.290][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.295][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.300][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.305][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.310][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.315][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:28.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:28.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.320][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:28.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:28.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.325][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:28.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:28.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.330][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-09 16:04:28.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.350][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-09 16:04:28.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:28.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.401][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.406][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.416][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:04:28.452][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-08-09 16:04:28.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:04:28.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:04:28.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:04:28.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:04:28.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.465][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-09 16:04:28.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-09 16:04:28.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-09 16:04:28.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-09 16:04:28.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.488][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.530][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.535][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.540][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-09 16:04:28.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.575][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.576][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.579][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:28.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:28.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.596][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.601][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.606][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.611][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.612][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.614][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.615][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:28.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.645][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.647][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.649][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:28.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.665][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.670][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.675][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.680][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.681][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.683][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.685][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:28.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.714][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.718][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:28.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.740][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.745][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.750][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.755][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.756][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.759][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.760][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:28.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.780][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.790][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.791][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.793][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:28.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:28.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.809][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:28.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:28.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.814][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:28.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:28.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.819][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:28.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:28.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.824][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:28.825][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:28.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.828][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.829][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:28.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:28.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.843][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:28.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:28.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.848][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:28.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:28.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:28.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:28.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.858][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:28.860][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:28.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.862][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:28.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:28.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.878][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.883][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.888][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.893][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.894][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.896][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.898][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:28.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.932][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.933][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.936][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:28.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.951][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.956][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.961][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.966][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.967][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.970][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.971][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:28.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.985][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.990][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:28.995][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.000][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:29.002][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:29.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.004][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:29.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:29.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.020][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.025][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.035][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.036][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.038][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.040][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.054][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:29.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:29.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.059][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:29.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:29.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.069][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:29.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:29.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.074][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:29.075][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:29.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.078][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.079][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:29.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:29.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:29.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:29.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:29.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:29.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.109][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:29.110][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:29.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.112][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:29.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:29.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.143][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.144][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.146][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.162][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.167][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.172][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.177][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.178][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.180][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.182][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.196][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:04:29.198][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:04:29.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.200][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.207][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-09 16:04:29.209][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-09 16:04:29.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.211][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.218][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.219][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:04:29.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.221][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.228][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-09 16:04:29.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-09 16:04:29.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.232][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.244][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:29.245][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-09 16:04:29.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.248][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.254][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:29.256][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-09 16:04:29.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.258][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.265][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.266][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-09 16:04:29.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.268][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.275][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:29.276][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-09 16:04:29.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.286][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:29.287][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:29.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.289][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.296][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:04:29.297][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:04:29.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.300][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.307][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:04:29.308][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:04:29.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.310][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.317][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.319][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:04:29.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.321][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.328][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:29.331][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-09 16:04:29.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.334][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:29.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-09 16:04:29.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.345][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.352][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:29.353][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:29.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.356][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.362][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:29.363][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-09 16:04:29.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.372][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:29.373][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:29.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.376][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.382][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-09 16:04:29.384][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-09 16:04:29.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.386][ef$get] fields variable is a list.
biodb.INFO [2025-08-09 16:04:29.398][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.399][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-09 16:04:29.400][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:29.401][biodb::testThat]
biodb.DEBUG[2025-08-09 16:04:29.419][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-09 16:04:29.439][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-09 16:04:29.442][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-09 16:04:29.468][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-09 16:04:29.471][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-09 16:04:29.472][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-09 16:04:29.512][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.514][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-09 16:04:29.515][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:29.516][biodb::testThat]
biodb.TRACE[2025-08-09 16:04:29.519][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:29.521][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:29.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.523][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:04:29.525][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-08-09 16:04:29.549][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-09 16:04:29.594][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-09 16:04:29.597][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-09 16:04:29.598][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-09 16:04:29.600][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-09 16:04:29.611][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-09 16:04:29.635][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.637][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-09 16:04:29.638][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:29.639][biodb::testThat]
biodb.DEBUG[2025-08-09 16:04:29.649][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-09 16:04:29.651][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-09 16:04:29.652][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-09 16:04:29.654][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-09 16:04:29.656][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-09 16:04:29.657][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-09 16:04:29.677][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.678][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-09 16:04:29.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:29.681][biodb::testThat]
biodb.DEBUG[2025-08-09 16:04:29.686][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-09 16:04:29.687][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-09 16:04:29.689][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-09 16:04:29.691][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-09 16:04:29.692][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-09 16:04:29.694][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-09 16:04:29.708][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.710][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-09 16:04:29.711][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:29.712][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.728][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.729][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-09 16:04:29.731][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:29.732][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.749][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.750][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-09 16:04:29.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:29.752][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.768][biodb::testThat]
biodb.INFO [2025-08-09 16:04:29.769][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-09 16:04:29.771][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:04:29.772][biodb::testThat]
biodb.TRACE[2025-08-09 16:04:29.798][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:29.800][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:29.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.802][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.808][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:29.810][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:29.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.812][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.813][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:29.814][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:29.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.817][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.818][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:04:29.819][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:04:29.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.822][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.823][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-09 16:04:29.824][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-09 16:04:29.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.827][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:04:29.828][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:29.829][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-09 16:04:29.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:04:29.831][ef$get] fields variable is a list.
biodb.INFO [2025-08-09 16:04:29.833][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-09 16:04:29.834][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-08-09 16:04:29.835][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-09 16:04:29.836][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:04:29.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:04:29.838][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:04:29.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:04:29.841][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:04:29.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbHmdb/DESCRIPTION' ... OK
* this is package 'biodbHmdb' version '1.15.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 'F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'zip'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'HmdbMetabolitesConn' 'HmdbMetabolitesEntry' 'hmdbToSqlite'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package 'biodbHmdb' ...
** this is package 'biodbHmdb' version '1.15.1'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -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"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbHmdb.dll tmp.def 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 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64
** 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
** 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)