Back to Long Tests report for BioC 3.22

This page was generated on 2025-08-30 23:55 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/29HostnameOS / ArchCHECK
biodbHmdb 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-30 09:55 -0400 (Sat, 30 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: fa89c02
git_last_commit_date: 2025-07-24 10:45:35 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on lconway

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

raw results


Summary

Package: biodbHmdb
Version: 1.15.1
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_1.15.1.tar.gz
StartedAt: 2025-08-30 16:01:08 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 16:02:07 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 58.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-08-30 16:02:04.723][biodb::testContext]
biodb.INFO [2025-08-30 16:02:04.725][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-30 16:02:04.726][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-30 16:02:04.727][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-30 16:02:04.728][biodb::testContext]
biodb.INFO [2025-08-30 16:02:04.732][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-30 16:02:04.733][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-30 16:02:04.738][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:02:04.739][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-30 16:02:04.740][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-30 16:02:04.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.743][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-30 16:02:04.756][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-30 16:02:04.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.759][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-30 16:02:04.759][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-30 16:02:04.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.762][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-30 16:02:04.763][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-30 16:02:04.764][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-30 16:02:04.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.766][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-30 16:02:04.767][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-30 16:02:04.768][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-30 16:02:04.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.771][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-30 16:02:04.772][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-30 16:02:04.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.775][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-30 16:02:04.775][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-30 16:02:04.776][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-30 16:02:04.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.779][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-30 16:02:04.780][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-30 16:02:04.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.782][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-30 16:02:04.783][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-30 16:02:04.784][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-30 16:02:04.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.787][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-30 16:02:04.787][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-30 16:02:04.788][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-30 16:02:04.789][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-30 16:02:04.790][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-30 16:02:04.791][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-30 16:02:04.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.794][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-30 16:02:04.794][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-30 16:02:04.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.797][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-30 16:02:04.798][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-30 16:02:04.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.801][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-30 16:02:04.802][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-30 16:02:04.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.804][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-30 16:02:04.805][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-30 16:02:04.806][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-30 16:02:04.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.808][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[2025-08-30 16:02:04.808][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-30 16:02:04.809][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-30 16:02:04.826][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-30 16:02:04.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.829][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-30 16:02:04.829][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-30 16:02:04.830][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-30 16:02:04.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.837][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[2025-08-30 16:02:04.839][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-30 16:02:04.862][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.873][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-30 16:02:04.874][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:04.875][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.876][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.877][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.878][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.878][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-30 16:02:04.879][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:04.880][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.881][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-30 16:02:04.881][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:04.882][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.883][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.884][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-30 16:02:04.884][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-30 16:02:04.884][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-30 16:02:04.884][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-30 16:02:04.884][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-30 16:02:04.885][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:02:04.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:04.886][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:04.887][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:04.888][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:04.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:04.889][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.890][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.890][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:04.891][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:04.892][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.892][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.893][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-30 16:02:04.895][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.895][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-30 16:02:04.896][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:04.898][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.898][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.899][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.900][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.901][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-30 16:02:04.901][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:04.902][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.903][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-30 16:02:04.903][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:04.904][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.905][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.906][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-30 16:02:04.906][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-30 16:02:04.906][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-30 16:02:04.906][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-30 16:02:04.906][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-30 16:02:04.906][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:02:04.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:04.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:04.908][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:04.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:04.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:04.911][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.911][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.912][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:04.913][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:04.914][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.914][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.915][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-30 16:02:04.917][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.918][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-30 16:02:04.918][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:04.920][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.921][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.922][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.922][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.923][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-30 16:02:04.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:04.925][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.926][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-30 16:02:04.926][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:04.927][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.928][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.929][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.930][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:02:04.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:04.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:04.932][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:04.932][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:04.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:04.934][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.935][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:04.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:04.937][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.938][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.939][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-30 16:02:04.940][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.941][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-30 16:02:04.941][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:04.943][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.943][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.944][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.945][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.946][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-30 16:02:04.946][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:04.947][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.948][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-30 16:02:04.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:04.949][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.950][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:04.951][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.952][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:02:04.952][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:04.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:04.954][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:04.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:04.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:04.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:04.956][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.957][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:04.958][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:04.958][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:04.959][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:04.962][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:02:04.963][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:04.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:04.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:04.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:04.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:04.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.025][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-30 16:02:05.028][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-30 16:02:05.029][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-30 16:02:05.031][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-30 16:02:05.032][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-30 16:02:05.033][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-30 16:02:05.034][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-30 16:02:05.035][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-30 16:02:05.036][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-30 16:02:05.037][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-30 16:02:05.038][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-30 16:02:05.040][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-30 16:02:05.041][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-30 16:02:05.042][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-30 16:02:05.043][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-30 16:02:05.044][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-30 16:02:05.045][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-30 16:02:05.046][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-30 16:02:05.047][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-30 16:02:05.048][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-30 16:02:05.049][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-30 16:02:05.050][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-30 16:02:05.052][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-30 16:02:05.053][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-30 16:02:05.054][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-30 16:02:05.055][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-30 16:02:05.056][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-30 16:02:05.057][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-30 16:02:05.058][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-30 16:02:05.059][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-30 16:02:05.060][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-30 16:02:05.061][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-30 16:02:05.062][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-30 16:02:05.064][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-30 16:02:05.065][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-30 16:02:05.066][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-30 16:02:05.067][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-30 16:02:05.068][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-30 16:02:05.069][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-30 16:02:05.070][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-30 16:02:05.071][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-30 16:02:05.072][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-30 16:02:05.073][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-30 16:02:05.075][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-30 16:02:05.076][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-30 16:02:05.077][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-30 16:02:05.078][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-30 16:02:05.079][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-30 16:02:05.080][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-30 16:02:05.081][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-30 16:02:05.083][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-30 16:02:05.084][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-30 16:02:05.085][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-30 16:02:05.086][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-30 16:02:05.087][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-30 16:02:05.088][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-30 16:02:05.089][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-30 16:02:05.090][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-30 16:02:05.092][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-30 16:02:05.093][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-30 16:02:05.094][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-30 16:02:05.095][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-30 16:02:05.096][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-30 16:02:05.097][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-30 16:02:05.098][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-30 16:02:05.099][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-30 16:02:05.100][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-30 16:02:05.101][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-30 16:02:05.102][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-30 16:02:05.103][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-30 16:02:05.104][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-30 16:02:05.109][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-30 16:02:05.110][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-30 16:02:05.111][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-30 16:02:05.112][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-30 16:02:05.114][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-30 16:02:05.115][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-30 16:02:05.116][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-30 16:02:05.117][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-30 16:02:05.118][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-30 16:02:05.119][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-30 16:02:05.121][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-30 16:02:05.122][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-30 16:02:05.126][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-30 16:02:05.128][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-30 16:02:05.130][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:02:05.131][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.132][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.170][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[2025-08-30 16:02:05.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-08-30 16:02:05.214][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-08-30 16:02:05.221][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-08-30 16:02:05.232][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-30 16:02:05.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:05.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:05.239][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-08-30 16:02:05.250][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-08-30 16:02:05.251][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:05.252][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-30 16:02:05.253][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:05.253][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:05.254][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:05.255][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-08-30 16:02:05.255][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:05.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:05.257][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-30 16:02:05.258][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:05.258][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:05.259][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-08-30 16:02:05.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-08-30 16:02:05.261][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-08-30 16:02:05.262][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:05.262][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-30 16:02:05.262][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-08-30 16:02:05.262][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-08-30 16:02:05.263][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-30 16:02:05.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:05.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:05.265][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:05.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:05.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:05.267][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:05.268][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-08-30 16:02:05.268][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-08-30 16:02:05.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:05.269][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:05.270][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:05.271][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:05.276][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-08-30 16:02:05.277][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-30 16:02:05.278][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-30 16:02:05.279][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-30 16:02:05.280][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-30 16:02:05.297][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-08-30 16:02:05.311][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-08-30 16:02:05.319][biodb::testThat]
biodb.INFO [2025-08-30 16:02:05.320][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-30 16:02:05.320][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:05.321][biodb::testThat]
biodb.TRACE[2025-08-30 16:02:05.325][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[2025-08-30 16:02:05.326][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-08-30 16:02:05.329][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-08-30 16:02:05.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-30 16:02:05.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:05.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:05.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:05.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:05.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:05.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-30 16:02:05.359][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.360][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.362][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.378][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.379][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.380][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.411][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.415][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.416][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.418][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.419][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.422][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.423][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.425][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.426][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.429][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.430][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.431][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.436][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.437][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.438][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.443][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.444][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.445][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.446][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.450][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.451][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.452][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.453][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.456][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.457][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.459][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.463][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.463][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.465][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.466][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.469][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:05.470][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:05.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.471][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.472][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:05.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:05.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.475][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:05.476][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:05.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.478][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:05.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:05.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.483][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.485][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.490][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.492][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.496][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.496][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.498][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.502][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:05.503][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:05.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.504][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.505][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:05.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:05.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.508][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:05.509][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:05.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.511][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.512][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:05.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:05.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.515][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-08-30 16:02:05.516][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:05.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.518][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.523][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-08-30 16:02:05.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:05.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.565][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.568][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.572][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:05.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.575][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.581][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:05.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:05.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.602][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:05.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.614][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.617][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:05.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.620][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:05.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:05.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.623][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:05.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:05.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.630][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:05.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:05.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.633][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:05.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:05.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.636][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:05.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:05.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.639][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:05.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:05.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.642][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:05.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:05.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.645][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:05.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:05.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:05.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:05.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:05.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:05.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:05.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:05.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:05.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:05.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.668][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.671][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:05.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:05.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.697][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.703][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.706][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.710][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.713][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.716][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:05.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:05.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:05.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:05.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.722][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:05.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:05.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.725][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-30 16:02:05.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.779][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-30 16:02:05.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:05.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.805][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:05.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:05.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.812][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.815][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.822][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-30 16:02:05.844][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-08-30 16:02:05.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:02:05.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:02:05.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.850][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:02:05.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:02:05.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.853][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-30 16:02:05.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-30 16:02:05.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.856][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-30 16:02:05.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-30 16:02:05.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.869][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.901][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.905][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.908][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-30 16:02:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.928][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.928][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.930][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:05.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:05.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.941][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.944][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.948][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.951][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.951][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.953][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.954][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:05.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.974][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.975][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.976][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:05.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.988][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.991][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.995][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:05.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:05.998][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:05.999][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:06.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.001][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.001][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:06.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:06.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.025][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.026][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.028][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.038][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.041][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.045][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.048][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.049][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.050][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.051][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.061][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.072][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.073][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.075][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.086][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:06.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:06.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.089][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:06.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:06.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.093][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:06.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:06.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.096][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:06.097][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:06.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.100][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:06.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:06.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:06.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:06.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.114][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:06.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:06.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:06.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:06.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.121][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:06.122][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:06.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.124][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.125][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:06.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:06.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.135][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.143][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.146][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.149][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.150][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.152][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.153][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.173][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.174][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.176][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.188][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.198][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.198][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.200][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.211][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.215][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.222][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.223][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.225][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.225][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.243][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.253][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.255][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.257][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.258][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.272][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:06.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:06.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.276][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:06.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:06.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.286][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:06.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:06.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.290][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:06.291][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:06.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.292][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.293][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:06.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:06.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:06.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:06.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:06.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:06.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:06.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:06.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.316][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:06.317][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:06.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.318][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:06.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:06.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.340][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.341][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.343][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.354][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.357][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.361][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.364][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.364][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.366][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.377][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:06.378][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:06.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.379][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.384][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.385][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-30 16:02:06.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.386][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.391][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.392][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:06.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.394][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.399][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.399][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-30 16:02:06.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.401][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.407][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:06.408][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-30 16:02:06.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.409][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.418][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.419][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-30 16:02:06.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.421][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.425][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.426][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-30 16:02:06.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.427][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.432][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.433][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-30 16:02:06.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.434][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.438][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:06.439][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:06.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.441][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.445][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:06.446][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:06.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.448][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.452][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:06.453][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:06.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.454][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.459][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.459][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:06.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.461][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.465][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.466][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-30 16:02:06.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.468][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.473][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-30 16:02:06.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.474][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.479][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.481][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.485][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:06.486][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-30 16:02:06.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.488][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.493][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:06.493][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:06.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.495][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.499][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-30 16:02:06.500][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-30 16:02:06.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.502][ef$get] fields variable is a list.
biodb.INFO [2025-08-30 16:02:06.509][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.509][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-30 16:02:06.510][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:06.511][biodb::testThat]
biodb.DEBUG[2025-08-30 16:02:06.521][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-30 16:02:06.526][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-30 16:02:06.528][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-30 16:02:06.554][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-30 16:02:06.555][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-30 16:02:06.556][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-30 16:02:06.586][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.587][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-30 16:02:06.587][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:06.588][biodb::testThat]
biodb.TRACE[2025-08-30 16:02:06.590][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.591][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.593][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-30 16:02:06.594][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-08-30 16:02:06.612][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-30 16:02:06.649][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-30 16:02:06.651][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-30 16:02:06.652][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-30 16:02:06.653][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-30 16:02:06.661][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-30 16:02:06.681][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.682][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-30 16:02:06.683][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:06.684][biodb::testThat]
biodb.DEBUG[2025-08-30 16:02:06.690][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-30 16:02:06.691][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-30 16:02:06.692][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-30 16:02:06.693][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-30 16:02:06.694][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-30 16:02:06.695][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-30 16:02:06.706][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.707][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-30 16:02:06.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:06.708][biodb::testThat]
biodb.DEBUG[2025-08-30 16:02:06.712][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-30 16:02:06.712][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-30 16:02:06.714][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-30 16:02:06.715][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-30 16:02:06.716][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-30 16:02:06.717][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-30 16:02:06.727][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.728][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-30 16:02:06.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:06.730][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.745][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.746][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-30 16:02:06.747][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:06.748][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.759][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.760][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-30 16:02:06.761][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:06.761][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.773][biodb::testThat]
biodb.INFO [2025-08-30 16:02:06.774][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-30 16:02:06.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:06.775][biodb::testThat]
biodb.TRACE[2025-08-30 16:02:06.796][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.797][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.798][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.799][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:06.800][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:06.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.801][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.802][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:06.803][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:06.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.804][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.805][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:06.806][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:06.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.807][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.808][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-30 16:02:06.809][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-30 16:02:06.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.810][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:06.811][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:06.812][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-30 16:02:06.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:06.813][ef$get] fields variable is a list.
biodb.INFO [2025-08-30 16:02:06.814][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-30 16:02:06.815][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-08-30 16:02:06.816][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-30 16:02:06.816][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:06.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:06.818][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:06.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:06.819][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:06.820][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".
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.15.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.15.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.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)