Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-01 23:55 -0400 (Sat, 01 Nov 2025).

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

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-11-01 09:55 -0400 (Sat, 01 Nov 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on nebbiolo2

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-11-01 16:01:09 -0400 (Sat, 01 Nov 2025)
EndedAt: 2025-11-01 16:02:17 -0400 (Sat, 01 Nov 2025)
EllapsedTime: 68.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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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 [2025-11-01 16:02:14.905][biodb::testContext]
biodb.INFO [2025-11-01 16:02:14.907][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:14.908][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-01 16:02:14.909][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:14.910][biodb::testContext]
biodb.INFO [2025-11-01 16:02:14.916][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:14.918][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:14.925][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:14.926][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:02:14.927][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:02:14.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:14.930][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:02:14.947][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:02:14.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.958][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:14.959][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:02:14.960][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:02:14.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:14.963][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:02:14.964][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:02:14.965][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:02:14.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.968][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:14.969][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:02:14.969][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:02:14.970][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:02:14.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:14.974][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:02:14.975][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:02:14.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.977][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[2025-11-01 16:02:14.978][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:02:14.979][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:02:14.980][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:02:14.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:14.983][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:02:14.984][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:02:14.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.987][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:14.988][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:02:14.989][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:02:14.990][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:02:14.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:14.993][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:14.994][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:02:14.995][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:02:14.996][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:02:14.997][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:02:14.998][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:02:14.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:14.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.001][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:02:15.002][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:02:15.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.005][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:02:15.006][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:02:15.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.009][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.010][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:02:15.011][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:02:15.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.014][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:02:15.015][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:02:15.016][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:02:15.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.018][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.019][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:15.020][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:02:15.023][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:02:15.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.026][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:02:15.027][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:02:15.028][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:02:15.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.031][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.034][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:02:15.064][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.079][self$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[2025-11-01 16:02:15.080][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.081][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:15.082][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.083][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.084][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.084][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.085][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:15.086][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:15.087][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.088][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:02:15.089][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:15.090][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.091][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.092][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:15.092][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:15.092][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:15.092][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:15.092][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:15.093][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:15.094][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.095][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.096][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:15.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.098][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.099][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.100][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:15.101][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:15.102][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.103][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.108][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:02:15.110][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.111][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:15.111][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.112][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:15.113][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.114][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.115][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.116][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.117][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:15.118][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:15.119][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.120][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:02:15.121][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:15.122][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.123][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.123][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:15.123][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:15.123][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:15.123][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:15.123][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:15.124][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:15.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.127][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:15.128][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.129][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.130][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.131][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.132][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:15.132][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:15.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.134][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.135][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:02:15.137][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.138][self$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[2025-11-01 16:02:15.139][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.140][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:15.141][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.141][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.142][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.143][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.144][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:15.145][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:15.146][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.147][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:02:15.148][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:15.149][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.150][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.151][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.152][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:15.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.154][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:15.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.157][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.158][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:15.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:15.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.161][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.162][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:02:15.164][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.165][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:15.166][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.167][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:15.168][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.169][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.170][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.171][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.171][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:15.172][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:15.173][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.174][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:02:15.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:15.176][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.177][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.178][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.179][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:15.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.181][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:15.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.184][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.185][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.186][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:15.187][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:15.188][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.189][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.192][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:15.193][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.194][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.198][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.202][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.206][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[2025-11-01 16:02:15.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.214][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.219][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.223][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.227][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[2025-11-01 16:02:15.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.231][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.235][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.239][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.252][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.256][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.263][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.264][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:02:15.269][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:02:15.270][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:02:15.271][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:02:15.273][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:02:15.274][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:15.275][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:15.276][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:15.278][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:02:15.279][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:15.280][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:15.282][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:02:15.283][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:15.284][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:15.286][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:15.287][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:15.288][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:02:15.289][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:02:15.291][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:02:15.292][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:02:15.293][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:02:15.295][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:02:15.296][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:02:15.297][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:02:15.298][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:02:15.300][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:02:15.301][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:02:15.302][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:02:15.304][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:02:15.305][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:02:15.306][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:02:15.308][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:02:15.309][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:02:15.310][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:02:15.311][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:02:15.313][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:02:15.314][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:02:15.315][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:02:15.317][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:02:15.318][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:02:15.319][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:02:15.320][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:02:15.322][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:02:15.323][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:02:15.324][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:02:15.326][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:15.327][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:02:15.328][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:02:15.330][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:02:15.331][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:02:15.332][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:02:15.339][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:02:15.341][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:02:15.343][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:02:15.344][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:02:15.346][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:02:15.347][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:02:15.349][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:02:15.350][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:02:15.352][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:02:15.353][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:02:15.355][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:02:15.356][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:02:15.358][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:02:15.359][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:02:15.361][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:02:15.362][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:02:15.363][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:02:15.365][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:02:15.366][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:02:15.368][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:02:15.369][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:02:15.371][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:02:15.372][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:02:15.373][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:02:15.375][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:02:15.376][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:02:15.378][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:02:15.379][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:02:15.381][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:02:15.382][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:02:15.384][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:02:15.385][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:02:15.392][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:02:15.394][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:15.398][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:15.398][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.400][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.412][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:15.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.438][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.445][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.451][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.458][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.464][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.470][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.477][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.483][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.489][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.495][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.502][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.508][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.514][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[2025-11-01 16:02:15.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.520][FUN] Functions in observer BiodbConfig: [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 [2025-11-01 16:02:15.521][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-11-01 16:02:15.530][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-11-01 16:02:15.542][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-11-01 16:02:15.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:15.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.548][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.550][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:15.559][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-11-01 16:02:15.560][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.561][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:15.564][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.565][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-11-01 16:02:15.566][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.568][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:15.569][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:15.570][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.571][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-11-01 16:02:15.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-11-01 16:02:15.573][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-11-01 16:02:15.574][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:15.575][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:15.575][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-11-01 16:02:15.575][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-11-01 16:02:15.576][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:15.576][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:15.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:15.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:15.581][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:15.582][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-11-01 16:02:15.582][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-11-01 16:02:15.587][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:15.587][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:15.588][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:15.589][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:15.595][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-11-01 16:02:15.596][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:15.598][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:15.599][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:15.600][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:15.621][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-11-01 16:02:15.636][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-11-01 16:02:15.643][biodb::testThat]
biodb.INFO [2025-11-01 16:02:15.644][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-01 16:02:15.645][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:15.646][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:15.650][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-11-01 16:02:15.651][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:15.655][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-11-01 16:02:15.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:15.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:15.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:15.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:15.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:15.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:15.678][FUN] Functions in observer BiodbConfig: [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[2025-11-01 16:02:15.689][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:15.690][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:15.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.692][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:15.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:15.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.709][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:15.710][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:15.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.712][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.736][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:15.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:15.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.740][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.741][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.743][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.745][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.757][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.758][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.760][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.761][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.765][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.766][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.768][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.773][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.774][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.775][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.781][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:15.782][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:15.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.783][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.784][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:15.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:15.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.788][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:15.789][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:15.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.791][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.792][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:15.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:15.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.796][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:15.797][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:15.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.799][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.800][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:15.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:15.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.804][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:15.805][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:15.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.807][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.808][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:15.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:15.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.812][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:15.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:15.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.814][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:15.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:15.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.819][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:15.820][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:15.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.822][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:15.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.827][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:15.828][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:15.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.830][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:15.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:15.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.835][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:15.836][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:15.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.837][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:15.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:15.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.842][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:15.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:15.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.845][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:15.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:15.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.850][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:15.851][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:15.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.853][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.854][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:15.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.858][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:15.859][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:15.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.860][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.861][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:15.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:15.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.865][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-11-01 16:02:15.866][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:15.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.868][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.869][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-11-01 16:02:15.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:15.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:15.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:15.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:15.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:15.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:15.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:15.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.955][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.959][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.963][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:15.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.966][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.970][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.974][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:15.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:15.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:15.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:15.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:15.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.000][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.025][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.029][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.033][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.037][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.040][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.044][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.051][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.081][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.085][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.089][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.115][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.118][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.122][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.126][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.129][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.133][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.140][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.148][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.151][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-01 16:02:16.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.159][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.166][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-01 16:02:16.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.206][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.210][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.217][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:16.243][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-11-01 16:02:16.250][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:16.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:16.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.254][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:16.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:16.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.262][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:16.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:16.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.265][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:16.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:16.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.278][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.309][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.316][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:16.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.337][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.338][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.339][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.351][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.354][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.358][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.362][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.363][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.365][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.365][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.390][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.391][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.393][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.404][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.408][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.412][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.415][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.416][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.418][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.419][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.440][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.441][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.443][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.454][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.458][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.465][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.466][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.468][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.469][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.494][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.495][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.496][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.507][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.511][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.515][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.519][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.520][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.521][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.522][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.532][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.543][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.544][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.546][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.557][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.561][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.564][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.568][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.569][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.571][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.572][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.593][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.594][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.596][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.610][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.614][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.617][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.621][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.622][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.624][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.635][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.639][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.642][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.646][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.647][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.649][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.663][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.671][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.672][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.674][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.684][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.688][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.692][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.696][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.697][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.698][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.699][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.724][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.725][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.727][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.749][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.751][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.762][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.766][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.770][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.773][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.774][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.776][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.777][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.787][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:16.788][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:16.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.790][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.794][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.795][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:16.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.796][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.800][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.801][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:16.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.803][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.807][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.808][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:16.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.809][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.813][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.814][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:16.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.816][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.820][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.821][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:16.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.822][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.826][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.827][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:16.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.829][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.836][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.837][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:16.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.839][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.843][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:16.844][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:16.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.846][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.849][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:16.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:16.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.852][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.856][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:16.857][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:16.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.859][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.863][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.864][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:16.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.865][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.870][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:16.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.872][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.876][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.877][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:16.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.878][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.882][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:16.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:16.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.885][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.889][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.890][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:16.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.891][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.895][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.896][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:16.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.898][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:16.902][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:16.903][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:16.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:16.905][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:16.911][biodb::testThat]
biodb.INFO [2025-11-01 16:02:16.912][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-01 16:02:16.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:16.913][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:16.926][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-01 16:02:16.929][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:16.931][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:16.963][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-01 16:02:16.964][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-01 16:02:16.965][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-11-01 16:02:17.000][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.001][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-01 16:02:17.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:17.003][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:17.006][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:17.007][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:17.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:17.009][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:17.010][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-11-01 16:02:17.029][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-01 16:02:17.077][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:17.079][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:17.080][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-01 16:02:17.081][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-01 16:02:17.093][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-11-01 16:02:17.115][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.117][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-01 16:02:17.117][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:17.118][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:17.125][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-01 16:02:17.126][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:17.127][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:17.128][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-01 16:02:17.129][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-01 16:02:17.130][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-11-01 16:02:17.142][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.147][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-01 16:02:17.148][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:17.149][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:17.152][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-01 16:02:17.153][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:17.154][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:17.155][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-01 16:02:17.156][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-01 16:02:17.157][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-11-01 16:02:17.169][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.170][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-01 16:02:17.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:17.172][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.184][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.185][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-01 16:02:17.185][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:17.186][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.199][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.200][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:17.201][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:17.202][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.214][biodb::testThat]
biodb.INFO [2025-11-01 16:02:17.215][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:17.216][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:17.217][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:17.242][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:17.243][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:17.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:17.248][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:17.249][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:17.250][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:17.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:17.252][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:17.253][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:17.254][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:17.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:17.256][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:17.257][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:17.258][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:17.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:17.260][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:17.261][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:17.262][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:17.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:17.263][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:17.264][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:17.265][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:17.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:17.267][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:17.268][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:02:17.269][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-11-01 16:02:17.270][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:02:17.271][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:17.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:17.273][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:17.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:17.274][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:17.275][FUN] Functions in observer 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:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   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
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)