Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-29 23:55 -0500 (Sat, 29 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4878
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4624
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: 2025-11-29 09:55 -0500 (Sat, 29 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 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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: 2025-11-29 16:01:15 -0500 (Sat, 29 Nov 2025)
EndedAt: 2025-11-29 16:02:50 -0500 (Sat, 29 Nov 2025)
EllapsedTime: 94.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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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 [2025-11-29 16:02:45.409][biodb::testContext]
biodb.INFO [2025-11-29 16:02:45.413][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-29 16:02:45.415][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-29 16:02:45.416][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-29 16:02:45.417][biodb::testContext]
biodb.INFO [2025-11-29 16:02:45.424][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-29 16:02:45.426][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-29 16:02:45.434][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-29 16:02:45.436][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-29 16:02:45.437][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-29 16:02:45.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.442][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-29 16:02:45.468][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-29 16:02:45.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.471][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.473][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-29 16:02:45.474][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-29 16:02:45.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.488][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-29 16:02:45.489][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-29 16:02:45.490][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-29 16:02:45.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.493][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.495][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-29 16:02:45.496][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-29 16:02:45.497][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-29 16:02:45.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.502][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-29 16:02:45.503][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-29 16:02:45.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.506][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.507][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-29 16:02:45.509][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-29 16:02:45.510][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-29 16:02:45.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.514][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-29 16:02:45.516][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-29 16:02:45.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.519][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.520][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-29 16:02:45.521][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-29 16:02:45.523][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-29 16:02:45.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.527][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-29 16:02:45.528][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-29 16:02:45.530][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-29 16:02:45.531][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-29 16:02:45.532][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-29 16:02:45.533][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-29 16:02:45.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.538][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-29 16:02:45.539][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-29 16:02:45.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.544][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-29 16:02:45.545][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-29 16:02:45.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.549][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-29 16:02:45.551][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-29 16:02:45.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.555][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-29 16:02:45.556][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-29 16:02:45.558][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-29 16:02:45.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.561][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.562][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-29 16:02:45.564][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-29 16:02:45.574][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-29 16:02:45.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.579][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-29 16:02:45.580][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-29 16:02:45.582][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-29 16:02:45.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.585][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.589][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-29 16:02:45.632][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.654][self$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[2025-11-29 16:02:45.656][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.657][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:45.658][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.660][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.661][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.662][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.663][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-29 16:02:45.665][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:45.666][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.667][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-29 16:02:45.669][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:45.670][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.671][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.672][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-29 16:02:45.672][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-29 16:02:45.672][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-29 16:02:45.672][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-29 16:02:45.672][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-29 16:02:45.674][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-29 16:02:45.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:45.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:45.677][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:45.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:45.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:45.681][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.682][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.683][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:45.684][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:45.686][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.687][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.688][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-29 16:02:45.691][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.692][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-29 16:02:45.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.694][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:45.696][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.697][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.698][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.700][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.701][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-29 16:02:45.702][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:45.708][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.709][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-29 16:02:45.710][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:45.712][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.713][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.714][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-29 16:02:45.714][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-29 16:02:45.714][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-29 16:02:45.714][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-29 16:02:45.714][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-29 16:02:45.716][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-29 16:02:45.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:45.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:45.719][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:45.720][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:45.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:45.723][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.724][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.725][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:45.726][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:45.727][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.729][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.730][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-29 16:02:45.732][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.733][self$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[2025-11-29 16:02:45.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.736][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:45.737][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.738][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.740][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.741][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.742][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-29 16:02:45.743][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:45.745][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.746][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-29 16:02:45.747][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:45.748][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.750][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.751][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.752][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-29 16:02:45.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:45.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:45.756][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:45.757][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:45.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:45.759][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.760][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.762][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:45.763][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:45.764][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.765][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.767][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-29 16:02:45.769][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.770][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-29 16:02:45.771][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.773][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:45.774][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.775][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.776][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.777][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.779][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-29 16:02:45.780][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:45.781][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.783][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-29 16:02:45.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:45.785][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.786][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:45.787][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.789][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-29 16:02:45.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:45.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:45.792][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:45.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:45.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:45.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:45.797][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:45.799][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:45.801][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:45.802][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:45.806][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-29 16:02:45.807][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.808][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.814][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.820][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.831][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.837][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.854][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.859][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.865][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.871][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:45.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.887][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.893][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:45.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:45.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:45.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:45.899][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:45.900][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-29 16:02:45.905][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-29 16:02:45.907][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-29 16:02:45.908][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-29 16:02:45.910][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-29 16:02:45.912][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-29 16:02:45.914][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-29 16:02:45.920][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-29 16:02:45.922][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-29 16:02:45.924][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-29 16:02:45.925][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-29 16:02:45.927][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-29 16:02:45.929][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-29 16:02:45.930][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-29 16:02:45.932][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-29 16:02:45.934][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-29 16:02:45.935][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-29 16:02:45.937][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-29 16:02:45.939][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-29 16:02:45.941][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-29 16:02:45.942][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-29 16:02:45.944][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-29 16:02:45.946][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-29 16:02:45.948][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-29 16:02:45.949][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-29 16:02:45.951][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-29 16:02:45.953][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-29 16:02:45.954][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-29 16:02:45.956][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-29 16:02:45.958][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-29 16:02:45.960][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-29 16:02:45.961][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-29 16:02:45.963][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-29 16:02:45.965][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-29 16:02:45.966][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-29 16:02:45.968][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-29 16:02:45.970][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-29 16:02:45.972][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-29 16:02:45.973][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-29 16:02:45.975][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-29 16:02:45.977][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-29 16:02:45.979][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-29 16:02:45.980][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-29 16:02:45.982][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-29 16:02:45.984][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-29 16:02:45.985][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-29 16:02:45.987][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-29 16:02:45.989][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-29 16:02:45.991][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-29 16:02:45.992][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-29 16:02:45.994][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-29 16:02:45.996][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-29 16:02:45.997][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-29 16:02:45.999][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-29 16:02:46.001][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-29 16:02:46.002][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-29 16:02:46.004][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-29 16:02:46.006][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-29 16:02:46.008][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-29 16:02:46.009][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-29 16:02:46.011][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-29 16:02:46.013][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-29 16:02:46.014][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-29 16:02:46.016][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-29 16:02:46.018][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-29 16:02:46.020][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-29 16:02:46.021][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-29 16:02:46.023][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-29 16:02:46.025][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-29 16:02:46.026][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-29 16:02:46.028][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-29 16:02:46.030][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-29 16:02:46.032][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-29 16:02:46.033][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-29 16:02:46.035][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-29 16:02:46.037][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-29 16:02:46.038][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-29 16:02:46.040][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-29 16:02:46.042][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-29 16:02:46.044][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-29 16:02:46.045][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-29 16:02:46.047][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-29 16:02:46.049][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-29 16:02:46.056][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-29 16:02:46.058][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-29 16:02:46.062][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-29 16:02:46.063][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.065][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:46.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:46.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:46.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.095][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[2025-11-29 16:02:46.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:46.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.110][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.123][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[2025-11-29 16:02:46.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.130][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.138][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:46.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.154][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.162][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.170][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.178][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.186][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-29 16:02:46.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-11-29 16:02:46.203][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-11-29 16:02:46.213][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-11-29 16:02:46.232][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-11-29 16:02:46.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-29 16:02:46.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.241][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.243][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-11-29 16:02:46.256][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-11-29 16:02:46.259][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:46.260][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-11-29 16:02:46.262][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:46.263][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-29 16:02:46.264][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:46.265][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-11-29 16:02:46.267][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:46.268][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-29 16:02:46.269][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-29 16:02:46.270][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-29 16:02:46.272][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:46.273][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-11-29 16:02:46.274][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-11-29 16:02:46.275][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-11-29 16:02:46.277][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-29 16:02:46.278][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-29 16:02:46.278][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-11-29 16:02:46.278][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-11-29 16:02:46.280][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-29 16:02:46.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:46.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:46.283][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-29 16:02:46.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-29 16:02:46.285][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-29 16:02:46.287][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-29 16:02:46.288][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-11-29 16:02:46.288][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-11-29 16:02:46.289][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-29 16:02:46.290][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-29 16:02:46.291][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-29 16:02:46.293][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-29 16:02:46.300][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-11-29 16:02:46.302][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-29 16:02:46.304][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-29 16:02:46.306][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-29 16:02:46.308][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-29 16:02:46.334][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-11-29 16:02:46.349][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-11-29 16:02:46.359][biodb::testThat]
biodb.INFO [2025-11-29 16:02:46.360][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-29 16:02:46.362][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:46.363][biodb::testThat]
biodb.TRACE[2025-11-29 16:02:46.367][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[2025-11-29 16:02:46.370][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-11-29 16:02:46.373][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-11-29 16:02:46.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-29 16:02:46.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:46.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:46.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:46.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:46.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:46.404][FUN] Functions in observer BiodbConfig: [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[2025-11-29 16:02:46.416][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:46.417][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:46.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.420][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:46.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:46.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.443][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:46.445][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:46.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.447][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.483][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:46.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:46.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.489][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.490][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.493][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.494][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.500][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.501][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.503][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.505][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.510][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.511][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.514][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.521][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.522][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.524][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.540][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.541][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.544][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.545][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.550][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.551][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.554][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.555][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.561][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.562][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.564][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.571][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.572][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.575][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.576][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.581][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:46.582][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:46.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.585][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.586][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:46.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:46.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.591][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:46.593][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:46.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.595][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:46.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:46.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.602][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.603][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.605][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.612][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.613][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.616][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.622][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:46.624][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:46.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.626][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:46.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:46.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.633][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:46.634][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:46.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.637][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.638][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:46.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:46.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.643][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:46.645][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:46.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.647][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.649][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:46.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:46.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.654][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-11-29 16:02:46.655][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:46.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.657][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.659][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-11-29 16:02:46.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:46.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:46.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:46.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:46.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:46.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:46.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:46.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.766][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.771][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.776][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:46.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.781][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.786][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.791][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:46.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:46.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:46.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.836][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:46.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.841][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.846][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.851][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:46.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.856][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:46.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:46.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.861][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:46.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:46.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:46.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:46.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.870][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:46.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:46.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.875][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:46.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:46.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.880][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:46.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:46.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:46.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:46.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:46.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:46.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.900][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:46.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:46.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:46.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:46.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:46.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:46.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:46.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:46.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.935][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.939][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.944][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:46.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:46.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:46.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:46.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.969][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:46.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:46.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:46.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:46.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.979][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.984][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:46.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.994][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:46.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:46.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:46.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:46.999][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.004][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.009][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:47.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:47.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.014][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:47.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:47.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.019][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:47.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:47.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.024][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-29 16:02:47.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.044][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-29 16:02:47.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.104][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.109][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.119][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-29 16:02:47.157][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-11-29 16:02:47.160][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-29 16:02:47.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-29 16:02:47.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.165][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-29 16:02:47.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-29 16:02:47.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.173][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-29 16:02:47.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-29 16:02:47.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-29 16:02:47.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-29 16:02:47.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.196][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.245][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.250][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.255][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-29 16:02:47.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.285][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.286][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.289][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.306][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.312][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.317][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.322][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.323][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.343][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.344][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:47.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.386][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.387][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.390][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:47.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.407][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.412][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.417][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.422][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.423][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.426][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.427][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:47.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.462][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.464][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.466][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:47.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.483][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.488][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.493][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.498][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.500][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.502][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.503][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:47.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.535][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.536][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.538][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:47.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:47.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.556][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:47.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:47.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.561][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:47.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:47.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.566][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:47.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:47.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.571][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:47.573][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:47.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.575][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.576][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:47.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:47.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.592][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:47.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:47.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.597][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:47.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:47.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.607][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:47.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:47.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.612][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:47.614][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:47.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.616][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.617][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:47.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:47.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.633][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.638][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.643][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.648][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.650][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.652][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.653][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.685][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.686][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.689][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:47.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.711][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.716][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.721][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.722][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.725][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.726][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:47.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.742][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.748][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.753][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.758][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.760][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.762][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.763][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:47.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.784][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.790][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.795][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.801][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.803][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.805][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:47.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.822][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:47.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:47.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.828][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:47.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:47.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:47.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:47.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.838][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:47.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:47.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.841][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.842][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:47.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:47.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:47.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:47.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:47.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:47.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:47.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.874][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:47.875][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:47.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.877][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:47.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:47.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.909][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.910][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.913][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:47.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.929][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.934][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.939][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.949][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.950][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.952][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.954][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.969][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-29 16:02:47.970][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-29 16:02:47.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.973][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.979][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.981][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-29 16:02:47.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.983][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:47.989][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.991][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-29 16:02:47.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:47.993][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-29 16:02:48.001][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-29 16:02:48.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.003][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.010][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:48.011][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-29 16:02:48.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.014][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.020][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:48.021][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-29 16:02:48.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.024][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.030][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:48.031][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-29 16:02:48.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.034][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.040][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:48.041][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-29 16:02:48.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.043][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.050][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:48.051][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:48.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.053][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.059][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-29 16:02:48.061][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-29 16:02:48.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.063][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.069][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-29 16:02:48.071][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-29 16:02:48.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.073][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-29 16:02:48.081][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-29 16:02:48.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.083][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.089][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:48.091][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-29 16:02:48.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.093][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:48.100][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-29 16:02:48.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.103][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.109][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:48.110][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:48.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.113][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.119][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:48.124][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-29 16:02:48.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.126][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.133][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:48.134][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:48.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.136][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:48.142][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-29 16:02:48.144][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-29 16:02:48.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.146][ef$get] fields variable is a list.
biodb.INFO [2025-11-29 16:02:48.156][biodb::testThat]
biodb.INFO [2025-11-29 16:02:48.157][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-29 16:02:48.159][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:48.160][biodb::testThat]
biodb.DEBUG[2025-11-29 16:02:48.178][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-29 16:02:48.181][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-29 16:02:48.185][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-29 16:02:48.225][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-29 16:02:48.227][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-29 16:02:48.228][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:48.403][biodb::testThat]
biodb.INFO [2025-11-29 16:02:48.405][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-29 16:02:48.406][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:48.407][biodb::testThat]
biodb.TRACE[2025-11-29 16:02:48.411][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:48.413][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:48.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:48.415][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-29 16:02:48.422][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-11-29 16:02:48.452][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-29 16:02:48.516][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-29 16:02:48.518][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-29 16:02:48.519][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-29 16:02:48.521][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-29 16:02:48.538][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:48.616][biodb::testThat]
biodb.INFO [2025-11-29 16:02:48.617][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-29 16:02:48.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:48.619][biodb::testThat]
biodb.DEBUG[2025-11-29 16:02:48.629][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-29 16:02:48.631][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-29 16:02:48.633][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-29 16:02:48.634][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-29 16:02:48.636][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-29 16:02:48.637][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:48.699][biodb::testThat]
biodb.INFO [2025-11-29 16:02:48.700][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-29 16:02:48.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:48.702][biodb::testThat]
biodb.DEBUG[2025-11-29 16:02:48.708][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-29 16:02:48.709][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-29 16:02:48.711][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-29 16:02:48.713][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-29 16:02:48.714][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-29 16:02:48.715][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:48.773][biodb::testThat]
biodb.INFO [2025-11-29 16:02:48.774][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-29 16:02:48.775][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:48.776][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:48.839][biodb::testThat]
biodb.INFO [2025-11-29 16:02:48.841][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-29 16:02:48.842][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:48.843][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:48.902][biodb::testThat]
biodb.INFO [2025-11-29 16:02:48.903][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-29 16:02:48.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:48.906][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-29 16:02:48.968][biodb::testThat]
biodb.INFO [2025-11-29 16:02:48.969][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-29 16:02:48.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-29 16:02:48.972][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-11-29 16:02:49.047][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:49.049][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:49.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:49.051][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:49.052][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:49.054][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:49.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:49.056][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:49.058][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:49.059][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:49.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:49.061][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:49.063][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-29 16:02:49.064][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-29 16:02:49.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:49.066][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:49.067][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-29 16:02:49.069][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-29 16:02:49.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:49.071][ef$get] fields variable is a list.
biodb.TRACE[2025-11-29 16:02:49.072][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:49.074][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-29 16:02:49.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-29 16:02:49.076][ef$get] fields variable is a list.
biodb.INFO [2025-11-29 16:02:49.077][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-29 16:02:49.079][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-11-29 16:02:49.080][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-29 16:02:49.081][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-29 16:02:49.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-29 16:02:49.083][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-29 16:02:49.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-29 16:02:49.090][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-29 16:02:49.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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 4.5.2 (2025-10-31)
* 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:
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

Status: 1 ERROR, 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)