Back to Long Tests report for BioC 3.22

This page was generated on 2025-08-16 23:55 -0400 (Sat, 16 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
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: 2025-08-16 09:55 -0400 (Sat, 16 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: 2025-08-16 16:01:10 -0400 (Sat, 16 Aug 2025)
EndedAt: 2025-08-16 16:02:15 -0400 (Sat, 16 Aug 2025)
EllapsedTime: 65.1 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 [2025-08-16 16:02:11.719][biodb::testContext]
biodb.INFO [2025-08-16 16:02:11.721][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:02:11.722][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-16 16:02:11.723][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:02:11.724][biodb::testContext]
biodb.INFO [2025-08-16 16:02:11.729][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:02:11.730][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-16 16:02:11.736][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:11.737][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-16 16:02:11.738][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-16 16:02:11.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:11.741][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-16 16:02:11.753][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-16 16:02:11.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.755][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.756][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-16 16:02:11.757][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-16 16:02:11.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:11.760][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-16 16:02:11.761][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-16 16:02:11.761][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-16 16:02:11.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.763][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.764][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-16 16:02:11.765][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-16 16:02:11.766][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-16 16:02:11.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:11.768][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-16 16:02:11.769][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-16 16:02:11.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.771][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.772][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-16 16:02:11.772][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-16 16:02:11.773][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-16 16:02:11.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:11.776][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-16 16:02:11.776][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-16 16:02:11.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.778][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[2025-08-16 16:02:11.779][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-16 16:02:11.780][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-16 16:02:11.780][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-16 16:02:11.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:11.783][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:02:11.784][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-16 16:02:11.785][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-16 16:02:11.785][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-16 16:02:11.786][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-16 16:02:11.787][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-16 16:02:11.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.789][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.789][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-16 16:02:11.790][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-16 16:02:11.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:11.793][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-16 16:02:11.794][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-16 16:02:11.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.796][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.797][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-16 16:02:11.797][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-16 16:02:11.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:11.801][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-16 16:02:11.801][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-16 16:02:11.802][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-16 16:02:11.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.804][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.805][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:02:11.806][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-16 16:02:11.824][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-16 16:02:11.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:11.827][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-16 16:02:11.828][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-16 16:02:11.829][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-16 16:02:11.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.835][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.838][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-16 16:02:11.862][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.874][self$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[2025-08-16 16:02:11.875][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.876][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:11.877][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.878][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.879][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.879][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.880][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:02:11.881][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:11.882][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.882][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-16 16:02:11.883][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:11.884][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.885][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.885][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:11.885][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:02:11.885][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:02:11.885][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:02:11.885][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:02:11.886][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:11.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:11.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:11.889][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:11.889][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:11.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:11.891][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.892][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:11.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:11.894][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.894][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.895][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-16 16:02:11.897][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.897][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:02:11.898][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.899][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:11.900][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.900][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.901][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.902][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.903][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:02:11.903][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:11.904][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.905][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-16 16:02:11.906][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:11.906][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.907][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.908][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:11.908][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:02:11.908][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:02:11.908][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:02:11.908][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:02:11.909][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:11.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:11.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:11.911][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:11.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:11.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:11.913][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.914][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.915][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:11.915][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:11.916][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.917][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.918][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-16 16:02:11.919][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.920][self$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[2025-08-16 16:02:11.921][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.922][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:11.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.923][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.924][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.925][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.926][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:02:11.927][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:11.927][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.928][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-16 16:02:11.929][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:11.930][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.931][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.932][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.932][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:11.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:11.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:11.935][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:11.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:11.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:11.937][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.938][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:11.939][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:11.940][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.941][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.942][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-16 16:02:11.943][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.944][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:02:11.945][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.945][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:11.946][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.948][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.949][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.950][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:02:11.951][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:11.952][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.952][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-16 16:02:11.953][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:11.954][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.955][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:11.956][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.957][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:11.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:11.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:11.959][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:11.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:11.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:11.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:11.963][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.964][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:11.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:11.965][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:11.966][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:11.969][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:11.970][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.971][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:11.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:11.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.980][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:11.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:11.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.984][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:11.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:11.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.988][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[2025-08-16 16:02:11.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:11.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:11.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.992][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[2025-08-16 16:02:11.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:11.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:11.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:11.996][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:11.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:11.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:11.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:11.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:12.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.004][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.008][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.012][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.017][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[2025-08-16 16:02:12.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.020][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.024][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[2025-08-16 16:02:12.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.028][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.032][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.035][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.039][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.040][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-16 16:02:12.044][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-16 16:02:12.045][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-16 16:02:12.046][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-16 16:02:12.047][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-16 16:02:12.048][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:02:12.050][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-16 16:02:12.051][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-16 16:02:12.052][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-16 16:02:12.053][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:02:12.054][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:02:12.055][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-16 16:02:12.056][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-16 16:02:12.057][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-16 16:02:12.058][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-16 16:02:12.059][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:02:12.061][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-16 16:02:12.062][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-16 16:02:12.063][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-16 16:02:12.064][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-16 16:02:12.065][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-16 16:02:12.066][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-16 16:02:12.067][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-16 16:02:12.069][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-16 16:02:12.070][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-16 16:02:12.071][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-16 16:02:12.072][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-16 16:02:12.073][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-16 16:02:12.074][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-16 16:02:12.075][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-16 16:02:12.076][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-16 16:02:12.077][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-16 16:02:12.078][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-16 16:02:12.079][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-16 16:02:12.080][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-16 16:02:12.081][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-16 16:02:12.082][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-16 16:02:12.083][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-16 16:02:12.085][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-16 16:02:12.086][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-16 16:02:12.087][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-16 16:02:12.088][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-16 16:02:12.089][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-16 16:02:12.090][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-16 16:02:12.091][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-16 16:02:12.092][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-16 16:02:12.093][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-16 16:02:12.094][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-16 16:02:12.096][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-16 16:02:12.097][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-16 16:02:12.098][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-16 16:02:12.099][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-16 16:02:12.100][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-16 16:02:12.101][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-16 16:02:12.102][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-16 16:02:12.103][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-16 16:02:12.104][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-16 16:02:12.105][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-16 16:02:12.106][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-16 16:02:12.108][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-16 16:02:12.109][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-16 16:02:12.110][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-16 16:02:12.111][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-16 16:02:12.112][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-16 16:02:12.113][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-16 16:02:12.114][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-16 16:02:12.115][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-16 16:02:12.116][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-16 16:02:12.117][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-16 16:02:12.118][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-16 16:02:12.120][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-16 16:02:12.125][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-16 16:02:12.126][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-16 16:02:12.127][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-16 16:02:12.128][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-16 16:02:12.129][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-16 16:02:12.131][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-16 16:02:12.132][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-16 16:02:12.133][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-16 16:02:12.134][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-16 16:02:12.135][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-16 16:02:12.137][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-16 16:02:12.138][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-16 16:02:12.143][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-16 16:02:12.144][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:02:12.147][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:12.148][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.149][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.150][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[2025-08-16 16:02:12.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.160][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[2025-08-16 16:02:12.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.166][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.171][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.176][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.182][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.187][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.192][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.197][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:12.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.207][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.212][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:12.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:12.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:12.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.232][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.237][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.WARN [2025-08-16 16:02:12.238][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-08-16 16:02:12.244][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-08-16 16:02:12.254][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-16 16:02:12.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:12.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.260][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.262][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-08-16 16:02:12.273][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-08-16 16:02:12.274][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:12.275][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-16 16:02:12.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:12.276][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:12.277][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:12.278][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-08-16 16:02:12.279][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:12.279][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:12.280][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-16 16:02:12.281][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:12.282][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:12.282][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-08-16 16:02:12.283][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-08-16 16:02:12.284][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-08-16 16:02:12.285][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:12.286][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:12.286][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-08-16 16:02:12.286][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-08-16 16:02:12.287][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-16 16:02:12.288][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:12.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:12.289][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:12.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:12.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:12.291][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:12.292][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-08-16 16:02:12.292][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-08-16 16:02:12.293][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:12.293][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:12.294][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:12.295][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:12.299][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-08-16 16:02:12.300][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:02:12.301][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:02:12.302][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:02:12.303][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:02:12.319][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-08-16 16:02:12.332][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-08-16 16:02:12.339][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.340][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-16 16:02:12.340][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.341][biodb::testThat]
biodb.TRACE[2025-08-16 16:02:12.344][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[2025-08-16 16:02:12.346][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-08-16 16:02:12.348][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-08-16 16:02:12.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:02:12.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.368][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:12.376][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.377][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.379][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.391][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.392][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.394][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.421][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.424][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.425][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.426][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.427][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.430][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.431][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.432][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.433][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.436][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.437][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.439][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.443][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.443][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.445][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.448][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.449][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.451][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.451][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.455][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.455][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.457][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.458][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.461][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.461][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.463][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.467][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.468][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.470][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.471][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.474][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:12.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:12.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.476][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.477][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:12.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:12.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.480][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:12.481][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:12.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.483][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:12.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:12.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.487][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.488][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.489][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.494][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.494][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.496][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.500][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.501][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.503][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.507][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:12.508][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:12.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.510][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.511][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:12.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:12.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.514][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:12.515][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:12.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.517][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.518][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:12.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:12.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.521][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-08-16 16:02:12.522][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.527][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.529][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-08-16 16:02:12.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.564][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.567][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.570][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.574][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.577][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.580][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.604][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.607][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.614][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.617][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.620][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.623][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.630][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.633][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:12.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:12.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.636][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:12.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:12.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.639][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:12.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:12.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.642][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:12.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:12.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.645][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:12.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:12.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.649][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:12.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:12.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:12.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:12.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:12.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:12.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:12.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:12.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.670][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.676][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.689][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.699][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.703][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.706][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.710][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.713][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.716][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.720][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:12.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:12.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.723][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:12.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:12.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:12.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.730][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-16 16:02:12.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.776][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-16 16:02:12.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.810][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.813][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.819][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:02:12.841][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-08-16 16:02:12.843][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:02:12.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:02:12.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.846][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:02:12.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:02:12.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.849][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:02:12.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:02:12.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.852][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:02:12.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:02:12.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.863][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.894][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.897][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.900][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:12.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.919][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.920][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.921][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.933][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.936][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.939][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.943][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.944][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.945][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.946][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.966][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.967][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.968][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.979][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.983][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.986][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.989][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.990][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.991][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.992][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.016][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.018][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.029][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.032][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.035][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.038][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.039][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.040][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.041][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.054][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.061][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.062][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.063][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.074][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:13.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:13.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.078][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:13.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:13.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.081][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:13.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:13.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.084][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:13.085][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:13.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.087][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.088][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:13.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:13.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:13.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:13.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:13.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:13.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.105][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:13.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:13.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.108][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:13.109][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:13.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.111][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:13.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:13.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.122][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.129][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.132][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.136][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.136][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.138][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.139][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.158][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.159][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.160][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.175][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.178][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.181][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.182][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.183][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.184][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.198][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.204][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.205][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.206][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.207][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.221][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.224][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.227][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.228][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.230][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.230][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.240][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:13.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:13.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.243][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:13.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:13.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.251][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:13.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:13.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.254][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:13.254][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:13.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.256][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.257][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:13.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:13.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:13.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:13.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:13.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:13.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:13.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:13.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.276][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:13.277][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:13.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:13.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:13.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.299][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.300][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.301][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.312][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.315][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.318][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.321][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.322][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.324][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.324][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.335][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:13.336][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:13.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.337][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.342][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.343][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:13.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.344][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.349][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.350][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:13.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.352][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.357][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:13.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.359][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.363][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:13.364][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:13.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.374][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.375][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:13.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.377][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.381][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.382][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:13.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.384][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.388][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.389][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:13.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.390][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.395][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:13.396][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:13.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.397][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.401][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:13.402][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:13.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.403][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.408][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:13.409][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:13.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.410][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.414][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.415][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:13.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.417][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.421][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.421][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:13.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.423][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.427][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.428][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:13.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.430][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.434][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.436][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.440][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:13.441][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:13.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.443][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.447][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:13.448][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:13.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.450][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.454][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:13.455][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:13.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.456][ef$get] fields variable is a list.
biodb.INFO [2025-08-16 16:02:13.463][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.464][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-16 16:02:13.465][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:13.466][biodb::testThat]
biodb.DEBUG[2025-08-16 16:02:13.477][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-16 16:02:13.482][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:13.484][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:13.511][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-16 16:02:13.512][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-16 16:02:13.513][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-16 16:02:13.543][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.544][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-16 16:02:13.544][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:13.545][biodb::testThat]
biodb.TRACE[2025-08-16 16:02:13.548][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.549][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.550][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:02:13.551][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-08-16 16:02:13.569][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-16 16:02:13.606][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:13.607][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:13.608][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-16 16:02:13.609][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-16 16:02:13.618][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-16 16:02:13.637][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.637][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-16 16:02:13.638][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:13.639][biodb::testThat]
biodb.DEBUG[2025-08-16 16:02:13.645][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-16 16:02:13.646][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:13.647][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:13.648][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-16 16:02:13.649][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-16 16:02:13.650][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-16 16:02:13.661][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.662][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-16 16:02:13.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:13.664][biodb::testThat]
biodb.DEBUG[2025-08-16 16:02:13.667][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-16 16:02:13.668][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:13.669][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:13.670][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-16 16:02:13.671][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-16 16:02:13.672][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-16 16:02:13.683][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.684][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-16 16:02:13.684][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:13.685][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.701][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.702][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-16 16:02:13.702][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:13.703][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.715][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.716][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-16 16:02:13.716][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:13.717][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.729][biodb::testThat]
biodb.INFO [2025-08-16 16:02:13.729][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-16 16:02:13.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:13.731][biodb::testThat]
biodb.TRACE[2025-08-16 16:02:13.751][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.752][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.754][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.754][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:13.755][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:13.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.757][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.758][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:13.758][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:13.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.760][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.760][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:13.761][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:13.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.763][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.764][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:13.764][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:13.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.766][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:13.767][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:13.767][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:13.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:13.769][ef$get] fields variable is a list.
biodb.INFO [2025-08-16 16:02:13.770][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-16 16:02:13.771][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-08-16 16:02:13.772][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-16 16:02:13.772][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:13.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:13.773][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:13.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:13.775][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:13.775][FUN] Functions in observer 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)