Back to Long Tests report for BioC 3.21

This page was generated on 2025-10-11 23:55 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
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 7/30HostnameOS / ArchCHECK
biodbHmdb 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-11 09:55 -0400 (Sat, 11 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_21
git_last_commit: a7f0a0f
git_last_commit_date: 2025-04-15 12:42:50 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.14.0.tar.gz
StartedAt: 2025-10-11 16:01:14 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 16:02:45 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 91.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-10-11 16:02:41.172][biodb::testContext]
biodb.INFO [2025-10-11 16:02:41.176][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:41.177][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-11 16:02:41.178][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:41.180][biodb::testContext]
biodb.INFO [2025-10-11 16:02:41.187][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:02:41.189][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:41.197][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:41.198][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:02:41.200][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:02:41.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.205][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:02:41.231][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:02:41.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.236][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:02:41.238][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:02:41.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.243][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:02:41.244][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:02:41.245][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:02:41.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.258][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.259][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:02:41.261][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:02:41.262][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:02:41.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.267][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:02:41.268][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:02:41.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.271][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.273][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:02:41.274][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:02:41.275][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:02:41.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.280][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:02:41.282][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:02:41.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.285][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.286][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:02:41.287][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:02:41.289][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:02:41.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.293][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:41.295][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:02:41.296][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:02:41.297][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:02:41.298][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:02:41.300][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:02:41.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.303][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.304][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:02:41.306][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:02:41.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.310][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:02:41.311][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:02:41.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.315][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.316][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:02:41.317][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:02:41.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.322][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:02:41.323][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:02:41.324][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:02:41.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.328][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.329][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:41.330][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:02:41.341][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:02:41.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.346][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:02:41.347][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:02:41.349][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:02:41.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.352][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.356][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:02:41.399][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.420][self$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[2025-10-11 16:02:41.422][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:41.424][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.427][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.428][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.429][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:41.431][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:41.432][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.433][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:02:41.435][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:41.436][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.437][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.438][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:41.438][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:41.438][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:41.438][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:41.438][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:41.440][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:41.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:41.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:41.443][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:41.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:41.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:41.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.448][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:41.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:41.452][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.453][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.455][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:02:41.457][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.458][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:41.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:41.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.463][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.465][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.466][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.467][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:41.468][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:41.470][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.471][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:02:41.478][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:41.479][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.480][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.482][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:41.482][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:41.482][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:41.482][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:41.482][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:41.483][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:41.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:41.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:41.487][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:41.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:41.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:41.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.492][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:41.494][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:41.496][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.497][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.499][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:02:41.501][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.503][self$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[2025-10-11 16:02:41.504][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:41.507][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.509][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.511][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.512][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:41.513][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:41.514][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.516][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:02:41.517][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:41.518][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.520][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.521][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.522][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:41.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:41.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:41.526][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:41.527][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:41.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:41.529][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.531][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.532][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:41.533][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:41.534][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.535][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.537][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:02:41.539][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.540][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:41.542][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.543][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:41.544][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.545][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.547][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.548][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.549][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:41.550][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:41.552][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.553][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:02:41.554][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:41.555][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.557][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:41.558][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.559][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:41.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:41.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:41.563][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:41.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:41.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:41.566][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:41.567][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.569][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:41.570][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:41.571][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:41.572][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:41.576][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:41.577][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.584][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.589][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.595][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.601][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.606][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.612][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.617][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.623][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.628][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.634][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.645][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.651][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.657][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.662][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.668][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.670][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:02:41.674][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:02:41.676][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:02:41.678][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:02:41.680][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:02:41.682][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:02:41.684][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:41.686][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:41.692][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:02:41.694][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:02:41.696][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:02:41.698][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:02:41.699][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:41.701][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:41.703][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:41.705][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:41.707][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:02:41.708][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:02:41.710][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:02:41.712][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:02:41.714][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:02:41.716][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:02:41.717][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:02:41.719][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:02:41.721][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:02:41.722][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:02:41.724][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:02:41.726][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:02:41.728][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:02:41.729][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:02:41.731][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:02:41.733][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:02:41.734][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:02:41.736][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:02:41.738][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:02:41.739][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:02:41.741][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:02:41.743][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:02:41.745][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:02:41.746][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:02:41.748][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:02:41.750][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:02:41.751][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:02:41.753][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:02:41.755][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:02:41.756][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:41.758][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:02:41.760][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:02:41.762][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:02:41.763][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:02:41.765][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:02:41.767][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:02:41.768][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:02:41.770][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:02:41.772][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:02:41.773][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:02:41.775][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:02:41.777][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:02:41.778][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:02:41.780][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:02:41.782][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:02:41.783][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:02:41.785][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:02:41.787][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:02:41.789][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:02:41.790][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:02:41.792][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:02:41.794][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:02:41.795][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:02:41.797][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:02:41.799][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:02:41.800][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:02:41.802][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:02:41.804][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:02:41.805][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:02:41.807][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:02:41.809][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:02:41.811][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:02:41.812][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:02:41.814][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:02:41.816][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:02:41.817][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:02:41.819][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:02:41.826][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:02:41.828][initialize] This is biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:02:41.832][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:41.833][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.835][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.836][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.851][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.858][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.866][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.874][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.894][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.902][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.909][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.917][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.933][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:41.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.949][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.957][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.964][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:41.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:41.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:41.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:41.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:41.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:41.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:41.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-10-11 16:02:41.973][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-10-11 16:02:41.983][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-10-11 16:02:42.002][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-10-11 16:02:42.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:42.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:42.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:42.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:42.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:42.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:42.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:42.013][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:42.025][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-10-11 16:02:42.027][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:42.029][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-10-11 16:02:42.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:42.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:42.032][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:42.034][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-10-11 16:02:42.035][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:42.036][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:42.037][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:42.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:42.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:42.041][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-10-11 16:02:42.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-10-11 16:02:42.044][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-10-11 16:02:42.045][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:42.047][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:42.047][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-10-11 16:02:42.047][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-10-11 16:02:42.048][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:42.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:42.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:42.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:42.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:42.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:42.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:42.056][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-10-11 16:02:42.056][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-10-11 16:02:42.057][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:42.058][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:42.060][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:42.061][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:42.069][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-10-11 16:02:42.071][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:02:42.073][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:02:42.075][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:02:42.077][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:42.103][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-10-11 16:02:42.120][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-10-11 16:02:42.129][biodb::testThat]
biodb.INFO [2025-10-11 16:02:42.131][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-11 16:02:42.132][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:42.133][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:42.138][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-10-11 16:02:42.140][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:02:42.144][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-10-11 16:02:42.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:02:42.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:42.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:42.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:42.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:42.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:42.173][FUN] Functions in observer BiodbConfig: [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[2025-10-11 16:02:42.185][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.186][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.189][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.211][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.213][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.215][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.251][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.256][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.257][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.260][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.261][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.267][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.268][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.270][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.272][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.277][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.278][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.281][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.287][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.289][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.291][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.307][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.308][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.310][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.312][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.317][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.318][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.321][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.322][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.327][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.328][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.331][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.337][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.339][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.341][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.343][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.348][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:42.349][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:42.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.351][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.353][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:42.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:42.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.358][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:42.359][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:42.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.361][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:42.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:42.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.368][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.369][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.371][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.378][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.379][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.381][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.388][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.389][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.391][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.398][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:42.399][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:42.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.401][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.403][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:42.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:42.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.408][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:42.409][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:42.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.412][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.413][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:42.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.418][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-10-11 16:02:42.420][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:42.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.425][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.428][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-10-11 16:02:42.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:42.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.536][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.542][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.547][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:42.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.552][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.556][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.561][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:42.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:42.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:42.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.596][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:42.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:42.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.626][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:42.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:42.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.631][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:42.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:42.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:42.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:42.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.641][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:42.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:42.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.646][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:42.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:42.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.651][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:42.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:42.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.656][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:42.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:42.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.664][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:42.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:42.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.669][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:42.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:42.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:42.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:42.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:42.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:42.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.684][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:42.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:42.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.704][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.709][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.714][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:42.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:42.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.749][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.754][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:42.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.765][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.770][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.775][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:42.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.780][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:42.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:42.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.786][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:42.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:42.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.792][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:42.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:42.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.797][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-11 16:02:42.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.820][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-10-11 16:02:42.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:42.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:42.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:42.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.877][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:42.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:42.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.882][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:42.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:42.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.891][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:42.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:42.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:42.925][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-10-11 16:02:42.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:42.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.933][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:42.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:42.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.938][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:42.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:42.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.943][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:42.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:42.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:42.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:42.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:42.986][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:42.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:42.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:42.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.097][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:43.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:43.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.107][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:43.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:43.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.117][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:43.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-10-11 16:02:43.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.169][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.171][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.176][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.193][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.198][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.203][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.208][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.210][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.212][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.213][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:43.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.243][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.245][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.247][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.263][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.268][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.273][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.284][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.285][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.287][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.289][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:43.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.319][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.320][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.323][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.338][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.344][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.349][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.354][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.355][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.357][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.359][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:43.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:43.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:43.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:43.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:43.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:43.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.390][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:43.391][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:43.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.393][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:43.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:43.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.410][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:43.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:43.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.415][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:43.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:43.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.420][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:43.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:43.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.425][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:43.426][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:43.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.428][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.430][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:43.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:43.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.449][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:43.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:43.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.454][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:43.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:43.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:43.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:43.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.464][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:43.465][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:43.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.468][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.469][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:43.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:43.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.484][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.489][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.494][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.499][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.500][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.503][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.504][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.534][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.536][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.538][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.569][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.571][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.573][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.589][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.595][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.600][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.605][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.606][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.608][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.614][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.628][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.634][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.639][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.643][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.645][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.647][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.648][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.663][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:43.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:43.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.668][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:43.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:43.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.673][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:43.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:43.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.678][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:43.680][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:43.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.683][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.685][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:43.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:43.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:43.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:43.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:43.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:43.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:43.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:43.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.736][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:43.738][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:43.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.741][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:43.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:43.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.784][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.804][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.813][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.818][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.823][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.825][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.827][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.828][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.843][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:43.845][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:43.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.847][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.853][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.855][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-10-11 16:02:43.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.857][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.863][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.865][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:43.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.867][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.874][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.875][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-10-11 16:02:43.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.878][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.884][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.885][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-10-11 16:02:43.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.888][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.894][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.896][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:43.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.898][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.904][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.906][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:43.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.908][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.915][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.916][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-10-11 16:02:43.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.918][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.925][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:43.926][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:43.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.929][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.935][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:43.937][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:43.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.939][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.945][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:43.947][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:43.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.949][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.956][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.957][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:43.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.959][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.966][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.967][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-10-11 16:02:43.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.969][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.976][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.977][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:43.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.980][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:43.990][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:43.991][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:43.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:43.994][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:44.000][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:44.002][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:44.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.004][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:44.011][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:44.012][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:44.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.015][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:44.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-10-11 16:02:44.022][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-10-11 16:02:44.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.025][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:02:44.035][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.037][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-11 16:02:44.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:44.039][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:44.058][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-11 16:02:44.061][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-11 16:02:44.064][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-11 16:02:44.104][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-11 16:02:44.106][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-11 16:02:44.107][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-11 16:02:44.163][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.165][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-11 16:02:44.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:44.167][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:44.171][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:44.173][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:44.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.175][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:44.177][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-10-11 16:02:44.207][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-11 16:02:44.270][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-11 16:02:44.272][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-11 16:02:44.274][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-11 16:02:44.276][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-11 16:02:44.298][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-11 16:02:44.332][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.334][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-11 16:02:44.335][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:44.336][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:44.346][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-11 16:02:44.347][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-11 16:02:44.349][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-11 16:02:44.351][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-11 16:02:44.353][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-11 16:02:44.354][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-11 16:02:44.372][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.373][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-11 16:02:44.375][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:44.376][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:44.381][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-10-11 16:02:44.382][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-11 16:02:44.384][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-10-11 16:02:44.385][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-10-11 16:02:44.387][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-10-11 16:02:44.388][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-10-11 16:02:44.406][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.407][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-11 16:02:44.408][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:44.410][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.428][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.430][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-11 16:02:44.431][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:44.432][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.455][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.457][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:44.458][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:44.459][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.478][biodb::testThat]
biodb.INFO [2025-10-11 16:02:44.479][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:44.480][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:44.481][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:44.518][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:44.519][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:44.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.522][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:44.523][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:44.524][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:44.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.526][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:44.528][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:44.529][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:44.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.531][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:44.533][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:44.534][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:44.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.536][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:44.538][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:44.539][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:44.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.541][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:44.542][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:44.544][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-10-11 16:02:44.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:44.546][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:02:44.547][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:02:44.549][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-10-11 16:02:44.550][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:02:44.551][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:44.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:44.553][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:44.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:44.556][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:44.557][FUN] Functions in observer 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 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-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.14.0’
** 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-3.21-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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)