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 lconway

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-11-01 16:01:14 -0400 (Sat, 01 Nov 2025)
EndedAt: 2025-11-01 16:02:15 -0400 (Sat, 01 Nov 2025)
EllapsedTime: 61.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-11-01 16:02:12.637][biodb::testContext]
biodb.INFO [2025-11-01 16:02:12.640][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:12.641][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-01 16:02:12.642][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:12.643][biodb::testContext]
biodb.INFO [2025-11-01 16:02:12.649][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:12.650][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:12.657][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:12.658][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:02:12.659][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:02:12.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.662][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:02:12.678][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:02:12.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.681][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:02:12.682][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:02:12.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.694][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:02:12.695][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:02:12.696][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:02:12.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.698][FUN] Functions in observer BiodbConfig: [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 16:02:12.698][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:02:12.699][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:02:12.700][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:02:12.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.703][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:02:12.704][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:02:12.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.707][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:02:12.708][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:02:12.709][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:02:12.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.712][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:02:12.713][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:02:12.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.715][FUN] Functions in observer BiodbConfig: [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 16:02:12.716][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:02:12.717][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:02:12.717][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:02:12.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.720][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:12.721][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:02:12.722][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:02:12.723][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:02:12.723][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:02:12.724][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:02:12.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.726][FUN] Functions in observer BiodbConfig: [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 16:02:12.727][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:02:12.728][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:02:12.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.731][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:02:12.732][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:02:12.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.733][FUN] Functions in observer BiodbConfig: [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 16:02:12.734][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:02:12.735][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:02:12.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.738][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:02:12.739][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:02:12.739][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:02:12.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.742][FUN] Functions in observer BiodbConfig: [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 16:02:12.742][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:12.743][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:02:12.763][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:02:12.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.766][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:02:12.767][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:02:12.768][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:02:12.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.770][FUN] Functions in observer BiodbConfig: [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 16:02:12.772][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:02:12.796][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.809][self$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 16:02:12.810][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.811][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:12.812][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.812][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.813][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.814][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.815][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:12.816][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:12.817][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.817][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:02:12.818][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:12.819][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.820][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.821][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:12.821][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:12.821][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:12.821][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:12.821][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:12.822][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:12.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:12.823][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:12.824][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:12.825][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:12.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:12.826][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.827][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.828][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:12.829][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:12.830][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.831][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.833][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:02:12.834][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.835][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:12.836][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.837][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:12.842][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.843][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.843][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.844][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.845][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:12.846][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:12.847][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.847][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:02:12.848][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:12.849][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.850][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.850][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:12.850][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:12.850][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:12.850][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:12.850][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:12.851][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:12.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:12.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:12.854][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:12.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:12.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:12.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.857][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.857][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:12.858][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:12.859][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.859][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.860][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:02:12.862][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.863][self$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 16:02:12.863][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:12.865][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.866][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.866][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.867][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.868][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:12.869][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:12.869][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.870][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:02:12.871][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:12.872][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.873][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.873][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.874][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:12.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:12.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:12.876][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:12.877][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:12.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:12.879][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.879][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.880][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:12.881][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:12.882][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.882][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.883][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:02:12.885][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.885][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:12.886][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.887][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:12.888][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.888][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.889][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.890][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.891][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:12.891][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:12.892][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.893][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:02:12.894][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:12.894][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.895][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:12.896][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.896][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:12.897][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:12.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:12.898][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:12.899][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:12.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:12.900][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:12.901][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.902][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:12.903][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:12.903][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:12.904][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:12.907][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:12.907][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.910][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 16:02:12.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.911][FUN] Functions in observer BiodbConfig: [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 16:02:12.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:12.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.915][FUN] Functions in observer BiodbConfig: [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 16:02:12.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.917][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 16:02:12.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:12.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.923][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 16:02:12.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.927][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 16:02:12.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.928][FUN] Functions in observer BiodbConfig: [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 16:02:12.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.930][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 16:02:12.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.933][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 16:02:12.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.937][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 16:02:12.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.938][FUN] Functions in observer BiodbConfig: [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 16:02:12.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.940][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 16:02:12.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.941][FUN] Functions in observer BiodbConfig: [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 16:02:12.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:12.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.945][FUN] Functions in observer BiodbConfig: [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 16:02:12.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.947][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 16:02:12.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:12.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.951][FUN] Functions in observer BiodbConfig: [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 16:02:12.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.953][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 16:02:12.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.957][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 16:02:12.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.958][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 16:02:12.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:12.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:12.960][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 16:02:12.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:12.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:12.962][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:02:12.969][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:02:12.970][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:02:12.971][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:02:12.972][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:02:12.973][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:12.974][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:12.975][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:12.976][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:02:12.977][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:12.978][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:12.979][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:02:12.980][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:12.981][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:12.982][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:12.983][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:12.984][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:02:12.985][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:02:12.986][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:02:12.987][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:02:12.988][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:02:12.989][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:02:12.990][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:02:12.991][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:02:12.992][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:02:12.993][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:02:12.994][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:02:12.995][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:02:12.996][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:02:12.997][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:02:12.999][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:02:13.000][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:02:13.001][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:02:13.002][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:02:13.003][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:02:13.004][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:02:13.005][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:02:13.006][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:02:13.007][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:02:13.008][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:02:13.009][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:02:13.010][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:02:13.011][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:02:13.012][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:02:13.013][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:02:13.014][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:13.015][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:02:13.016][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:02:13.017][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:02:13.018][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:02:13.019][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:02:13.020][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:02:13.021][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:02:13.022][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:02:13.023][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:02:13.024][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:02:13.025][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:02:13.026][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:02:13.027][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:02:13.028][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:02:13.029][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:02:13.030][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:02:13.031][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:02:13.032][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:02:13.033][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:02:13.034][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:02:13.035][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:02:13.036][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:02:13.037][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:02:13.038][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:02:13.039][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:02:13.040][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:02:13.041][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:02:13.042][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:02:13.043][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:02:13.044][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:02:13.045][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:02:13.046][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:02:13.047][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:02:13.048][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:02:13.049][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:02:13.050][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:02:13.051][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:02:13.055][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:02:13.056][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:13.058][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:13.059][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.059][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 16:02:13.060][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.061][FUN] Functions in observer BiodbConfig: [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 16:02:13.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.067][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 16:02:13.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.068][FUN] Functions in observer BiodbConfig: [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 16:02:13.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.071][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 16:02:13.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.072][FUN] Functions in observer BiodbConfig: [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 16:02:13.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.076][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 16:02:13.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.077][FUN] Functions in observer BiodbConfig: [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 16:02:13.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.080][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 16:02:13.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.086][FUN] Functions in observer BiodbConfig: [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 16:02:13.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.089][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 16:02:13.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.090][FUN] Functions in observer BiodbConfig: [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 16:02:13.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.093][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 16:02:13.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.095][FUN] Functions in observer BiodbConfig: [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 16:02:13.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:13.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.099][FUN] Functions in observer BiodbConfig: [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 16:02:13.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.103][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 16:02:13.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:13.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.108][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 16:02:13.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.109][FUN] Functions in observer BiodbConfig: [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 16:02:13.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.112][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 16:02:13.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.114][FUN] Functions in observer BiodbConfig: [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 16:02:13.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.117][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 16:02:13.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.118][FUN] Functions in observer BiodbConfig: [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 16:02:13.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.122][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 16:02:13.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.123][FUN] Functions in observer BiodbConfig: [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 16:02:13.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.126][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 16:02:13.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:13.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.131][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 16:02:13.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.132][FUN] Functions in observer BiodbConfig: [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 16:02:13.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:13.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.137][FUN] Functions in observer BiodbConfig: [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 16:02:13.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:13.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-11-01 16:02:13.142][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-11-01 16:02:13.148][private$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 16:02:13.158][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-11-01 16:02:13.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:13.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.162][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 16:02:13.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.163][FUN] Functions in observer BiodbConfig: [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 16:02:13.165][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:13.172][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-11-01 16:02:13.173][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:13.174][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-11-01 16:02:13.175][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:13.175][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:13.176][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:13.177][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-11-01 16:02:13.178][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:13.178][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:13.179][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-01 16:02:13.180][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:13.181][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:13.181][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-11-01 16:02:13.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-11-01 16:02:13.183][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-11-01 16:02:13.184][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:13.185][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:13.185][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-11-01 16:02:13.185][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-11-01 16:02:13.185][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:13.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:13.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:13.187][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:13.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:13.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:13.189][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:13.190][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-11-01 16:02:13.190][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-11-01 16:02:13.191][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:13.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:13.192][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:13.193][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:13.201][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-11-01 16:02:13.202][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:13.203][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:13.204][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:13.205][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:13.222][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-11-01 16:02:13.233][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-11-01 16:02:13.240][biodb::testThat]
biodb.INFO [2025-11-01 16:02:13.241][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-01 16:02:13.242][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:13.242][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:13.245][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-11-01 16:02:13.247][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:13.249][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-11-01 16:02:13.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:13.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:13.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:13.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:13.268][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 16:02:13.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:13.270][FUN] Functions in observer BiodbConfig: [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 16:02:13.278][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.279][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.281][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.294][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.295][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.297][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.315][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.318][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.319][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.320][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.321][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.324][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.325][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.326][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.327][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.330][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.341][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.345][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.346][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.347][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.352][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.352][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.354][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.355][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.358][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.359][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.361][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.362][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.365][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.365][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.367][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.368][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.371][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.372][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.374][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.375][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.378][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:13.379][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:13.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.380][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.381][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:13.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:13.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.385][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:13.386][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:13.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.387][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:13.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:13.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.392][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.393][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.394][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.399][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.399][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.401][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.406][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.408][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.413][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.414][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.416][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.417][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.421][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:13.422][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:13.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.424][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.425][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:13.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:13.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.429][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-11-01 16:02:13.430][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:13.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.431][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.433][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-11-01 16:02:13.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:13.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.518][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.522][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.525][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:13.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.528][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.532][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.535][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:13.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.562][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:13.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.565][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.567][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:13.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.573][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:13.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:13.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.576][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:13.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:13.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.579][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:13.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:13.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.586][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.588][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.591][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.594][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:13.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:13.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.597][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:13.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:13.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.600][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:13.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:13.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:13.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:13.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:13.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:13.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:13.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:13.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.620][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.623][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.626][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:13.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.647][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.650][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.652][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.655][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.658][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.661][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.664][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:13.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:13.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.667][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:13.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:13.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.670][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:13.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:13.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.673][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-01 16:02:13.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.688][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-01 16:02:13.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:13.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.717][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.720][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.726][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:13.746][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-11-01 16:02:13.748][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:13.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:13.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.751][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:13.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:13.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:13.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:13.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.771][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.804][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-01 16:02:13.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.822][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.823][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.825][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:13.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:13.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.835][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.838][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.841][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.844][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.845][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.846][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.847][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:13.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.865][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.866][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.867][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:13.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.882][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.885][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.888][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.891][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.892][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.893][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.894][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:13.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.913][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.915][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:13.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.926][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.929][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.932][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.934][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.935][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.937][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.937][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:13.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.956][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.956][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.958][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:13.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:13.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.975][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.978][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.981][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.982][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.983][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.984][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:13.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:13.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.994][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:13.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:13.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.996][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:13.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:13.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:13.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:13.999][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:14.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:14.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.002][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:14.003][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:14.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.005][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.005][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:14.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:14.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.015][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.018][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.021][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.024][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.024][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.026][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.026][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.045][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.046][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.048][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.059][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.062][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.065][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.069][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.069][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.071][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.088][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.095][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.096][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.097][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.107][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.110][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.114][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.116][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.117][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.119][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.129][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:14.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:14.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.132][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:14.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:14.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.136][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:14.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:14.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.139][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:14.139][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:14.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.141][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.141][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:14.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:14.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.151][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:14.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:14.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:14.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:14.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:14.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:14.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.160][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:14.161][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:14.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.162][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:14.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:14.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.173][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.186][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.187][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.188][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.199][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.202][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.205][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.207][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.208][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.210][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.210][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.220][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:14.221][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:14.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.222][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.226][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.227][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-01 16:02:14.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.229][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.233][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.234][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:14.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.235][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.240][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-01 16:02:14.241][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-01 16:02:14.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.242][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.246][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:14.247][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-01 16:02:14.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.248][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.252][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.253][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-01 16:02:14.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.255][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.259][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.259][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-01 16:02:14.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.261][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.265][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.266][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-01 16:02:14.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.267][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.271][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:14.272][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:14.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.274][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.278][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:14.279][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:14.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.280][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.284][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:14.289][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:14.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.291][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.295][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.295][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:14.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.297][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.301][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:14.302][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-01 16:02:14.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.303][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.308][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.308][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-01 16:02:14.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.310][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.314][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:14.315][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:14.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.316][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.320][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:14.321][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-01 16:02:14.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.322][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.326][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:14.327][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:14.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.328][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.333][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-01 16:02:14.333][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-01 16:02:14.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.335][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:14.342][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.342][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-01 16:02:14.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:14.344][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:14.353][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-01 16:02:14.357][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:14.359][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:14.379][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-01 16:02:14.380][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-01 16:02:14.381][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-11-01 16:02:14.413][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.415][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-01 16:02:14.416][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:14.417][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:14.421][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:14.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:14.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.423][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:14.424][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-11-01 16:02:14.441][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-01 16:02:14.477][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:14.478][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:14.479][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-01 16:02:14.480][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-01 16:02:14.489][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-11-01 16:02:14.507][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.508][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-01 16:02:14.508][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:14.509][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:14.515][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-01 16:02:14.516][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:14.517][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:14.518][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-01 16:02:14.519][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-01 16:02:14.520][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-11-01 16:02:14.530][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.530][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-01 16:02:14.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:14.532][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:14.535][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-01 16:02:14.535][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:14.536][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:14.537][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-01 16:02:14.538][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-01 16:02:14.539][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-11-01 16:02:14.549][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.550][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-01 16:02:14.551][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:14.551][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.566][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.567][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-01 16:02:14.568][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:14.569][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.580][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.581][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:14.582][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:14.583][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.594][biodb::testThat]
biodb.INFO [2025-11-01 16:02:14.595][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:14.596][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:14.596][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:14.617][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:14.618][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:14.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.619][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.620][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:14.621][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:14.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.622][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.623][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:14.623][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:14.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.625][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.626][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:14.626][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:14.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.628][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.629][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-01 16:02:14.629][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-01 16:02:14.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.631][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:14.631][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:14.632][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-01 16:02:14.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:14.634][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:14.634][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:02:14.635][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-11-01 16:02:14.636][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:02:14.636][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:14.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:14.638][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:14.639][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 16:02:14.639][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:14.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)