Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-22 23:55 -0500 (Sat, 22 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4873
merida1macOS 12.7.6 Montereyx86_644.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" 4654
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 5/31HostnameOS / ArchCHECK
biodbChebi 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-11-22 09:55 -0500 (Sat, 22 Nov 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_22
git_last_commit: 28c1b2d
git_last_commit_date: 2025-10-29 11:12:25 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbChebi on merida1

To the developers/maintainers of the biodbChebi 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: biodbChebi
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbChebi_1.16.0.tar.gz
StartedAt: 2025-11-22 16:01:58 -0500 (Sat, 22 Nov 2025)
EndedAt: 2025-11-22 16:03:30 -0500 (Sat, 22 Nov 2025)
EllapsedTime: 91.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbChebi.Rcheck
Warnings: NA

Tests output

biodbChebi.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-11-22 16:02:51.147][biodb::testContext]
biodb.INFO [2025-11-22 16:02:51.151][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:02:51.152][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-22 16:02:51.154][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:02:51.155][biodb::testContext]
biodb.INFO [2025-11-22 16:02:51.161][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:02:51.165][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:02:51.173][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:02:51.175][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:02:51.176][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:02:51.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.181][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:02:51.207][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:02:51.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.212][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:02:51.213][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:02:51.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.218][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:02:51.219][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:02:51.221][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:02:51.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.226][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:02:51.227][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:02:51.237][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:02:51.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.242][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:02:51.243][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:02:51.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.247][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:02:51.249][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:02:51.250][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:02:51.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.255][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:02:51.256][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:02:51.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.260][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:02:51.262][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:02:51.263][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:02:51.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.268][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:02:51.269][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:02:51.270][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:02:51.271][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:02:51.273][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:02:51.274][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:02:51.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.278][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:02:51.280][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:02:51.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.284][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:02:51.285][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:02:51.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.290][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:02:51.291][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:02:51.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.296][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:02:51.297][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:02:51.298][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:02:51.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.303][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:02:51.304][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:02:51.315][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:02:51.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.320][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:02:51.321][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:02:51.323][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:02:51.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.330][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:02:51.373][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.395][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:02:51.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.397][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:51.399][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.400][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.401][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.402][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.404][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:02:51.405][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:51.406][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.407][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:02:51.409][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:51.410][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.411][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.412][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:02:51.412][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:02:51.412][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:02:51.412][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:02:51.412][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:02:51.414][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:02:51.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.417][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:51.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.421][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.422][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:51.424][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:51.426][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.427][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.428][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:02:51.430][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.432][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:02:51.433][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.434][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:51.436][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.437][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.438][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.439][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.440][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:02:51.442][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:51.443][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.444][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:02:51.446][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:51.447][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.448][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.449][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:02:51.449][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:02:51.449][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:02:51.449][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:02:51.449][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:02:51.451][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:02:51.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.453][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.454][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:51.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.462][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.463][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.464][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.465][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:51.466][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:51.468][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.469][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.470][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:02:51.473][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.474][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:02:51.475][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.476][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:51.478][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.480][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.482][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.483][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:02:51.484][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:51.486][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.488][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:02:51.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:51.492][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.493][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.494][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.496][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:02:51.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.499][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:51.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.504][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.505][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:51.507][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:51.508][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.509][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.511][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:02:51.513][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.514][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:02:51.516][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.517][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:51.519][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.520][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.521][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.522][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.524][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:02:51.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:51.526][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.527][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:02:51.529][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:51.530][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.531][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.533][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.534][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:02:51.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.538][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:51.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.541][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.543][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.544][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:51.545][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:51.546][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.547][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:51.552][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:02:51.553][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.589][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[2025-11-22 16:02:51.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.595][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[2025-11-22 16:02:51.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.606][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[2025-11-22 16:02:51.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.612][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[2025-11-22 16:02:51.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.623][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[2025-11-22 16:02:51.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.634][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[2025-11-22 16:02:51.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.640][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[2025-11-22 16:02:51.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.647][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:02:51.652][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:02:51.653][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:02:51.655][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:02:51.657][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:02:51.658][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:02:51.660][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:02:51.662][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:02:51.664][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:02:51.666][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:02:51.668][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:02:51.669][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:02:51.671][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:02:51.673][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:02:51.674][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:02:51.676][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:02:51.682][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:02:51.684][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:02:51.686][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:02:51.688][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:02:51.690][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:02:51.691][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:02:51.693][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:02:51.695][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:02:51.697][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:02:51.698][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:02:51.700][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:02:51.702][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:02:51.704][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:02:51.705][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:02:51.707][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:02:51.709][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:02:51.710][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:02:51.712][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:02:51.714][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:02:51.716][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:02:51.717][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:02:51.719][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:02:51.721][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:02:51.722][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:02:51.724][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:02:51.726][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:02:51.727][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:02:51.729][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:02:51.731][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:02:51.733][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:02:51.734][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:02:51.736][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:02:51.738][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:02:51.739][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:02:51.741][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:02:51.743][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:02:51.745][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:02:51.746][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:02:51.748][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:02:51.750][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:02:51.751][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:02:51.753][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:02:51.755][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:02:51.756][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:02:51.758][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:02:51.760][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:02:51.761][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:02:51.763][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:02:51.765][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:02:51.767][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:02:51.768][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:02:51.770][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:02:51.772][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:02:51.773][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:02:51.775][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:02:51.777][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:02:51.778][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:02:51.780][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:02:51.782][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:02:51.783][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:02:51.785][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:02:51.787][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:02:51.789][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:02:51.790][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:02:51.792][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:02:51.794][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:02:51.795][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:02:51.803][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:02:51.805][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:02:51.808][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:02:51.809][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.811][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:51.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:51.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:51.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:51.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:51.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:51.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:51.949][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/definitions.yml".
biodb.DEBUG[2025-11-22 16:02:51.961][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-11-22 16:02:51.964][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.965][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.966][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.968][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:51.969][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.970][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.972][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.973][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-11-22 16:02:51.974][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:02:51.975][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:51.977][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.978][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-11-22 16:02:51.979][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-11-22 16:02:51.981][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-11-22 16:02:51.982][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:51.983][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:02:51.983][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:02:51.983][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:02:51.985][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:02:51.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.988][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:51.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:51.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:51.992][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:51.993][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-11-22 16:02:51.993][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-11-22 16:02:51.994][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:51.995][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:51.997][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:51.998][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-11-22 16:02:51.998][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-11-22 16:02:52.006][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:02:52.008][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:02:52.010][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-11-22 16:02:52.012][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:02:52.014][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:02:52.015][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:02:52.038][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-11-22 16:02:52.056][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-11-22 16:02:52.065][biodb::testThat]
biodb.INFO [2025-11-22 16:02:52.067][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-22 16:02:52.068][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:52.069][biodb::testThat]
biodb.TRACE[2025-11-22 16:02:52.073][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-11-22 16:02:52.076][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:02:52.080][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-11-22 16:02:52.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:52.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:52.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:52.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:52.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:52.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:52.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:02:52.131][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.134][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.157][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:52.159][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:52.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.161][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.197][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:52.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:52.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.203][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:52.204][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:52.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.207][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:52.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:52.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.213][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:52.215][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:52.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.217][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:52.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:52.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.224][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.225][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.228][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.234][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.236][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.238][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.240][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.245][ef$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:52.246][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.248][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.250][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:52.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.255][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.257][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.259][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.266][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:52.267][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:52.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.269][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:52.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:52.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.276][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:02:52.278][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.280][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.287][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:02:52.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.292][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:52.293][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:52.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.296][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:52.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:52.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:52.399][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-11-22 16:02:52.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:52.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:52.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:52.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:52.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.505][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:02:52.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:02:52.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.510][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:02:52.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:02:52.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.515][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:02:52.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:02:52.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.520][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:02:52.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:02:52.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.630][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.632][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.634][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:52.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:52.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.670][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.674][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:52.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:52.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:52.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:52.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:52.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.705][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:52.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:52.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.709][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:52.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:52.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.726][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:52.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:52.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.731][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:52.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:52.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.736][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:52.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:52.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.741][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:52.742][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:52.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.745][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:52.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:52.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.777][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.778][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.781][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:52.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.813][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.815][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.817][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:52.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.838][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:52.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:52.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.845][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:52.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:52.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.850][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:52.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:52.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.855][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:52.857][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:52.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.859][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.861][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:52.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:52.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.876][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.881][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.886][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.891][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.893][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.895][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.897][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:52.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.911][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.917][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.922][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.927][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.928][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.930][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.932][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:52.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:52.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:52.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.953][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:52.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:52.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.958][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:52.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:52.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.964][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:52.965][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:52.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.967][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.969][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:52.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:52.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.984][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:52.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:52.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:52.999][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.005][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.008][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.039][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.040][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.043][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.059][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.061][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.063][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.070][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:53.071][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:53.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.074][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.080][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:53.082][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:53.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.084][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.090][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.092][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.094][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.102][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.104][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.111][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.112][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.115][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.121][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.123][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.125][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.132][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.133][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.136][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.142][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.144][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.146][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.153][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:53.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:53.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.157][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.164][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:53.165][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:53.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.167][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.195][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-2528-content.xml".
biodb.DEBUG[2025-11-22 16:02:53.244][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:02:53.245][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-11-22 16:02:53.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:53.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:53.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:53.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:53.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:53.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:53.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:02:53.263][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.264][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.266][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.296][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:53.297][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:53.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.300][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.301][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:53.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:53.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.307][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:53.308][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:53.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.310][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:53.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:53.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.318][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.319][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.322][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.328][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.330][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.332][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.339][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.345][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.348][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.349][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.354][ef$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:53.356][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.358][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.360][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:53.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.365][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.369][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.375][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:53.377][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:53.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.379][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:53.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:53.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.386][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:02:53.387][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.390][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.391][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:02:53.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.397][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:53.398][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:53.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.400][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.402][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:53.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:53.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:53.459][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2528.
biodb.TRACE[2025-11-22 16:02:53.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:53.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:53.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:53.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.523][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:02:53.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:02:53.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:02:53.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:02:53.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.534][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:02:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:02:53.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.540][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:02:53.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:02:53.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.658][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.661][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:53.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.698][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.700][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.702][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:53.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:53.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:53.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:53.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:53.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:53.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:53.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.735][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:53.736][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:53.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.739][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:53.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:53.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:53.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:53.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:53.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:53.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:53.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.772][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:53.773][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:53.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.775][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:53.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:53.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.792][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:53.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.808][ef$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:53.809][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.811][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.813][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:53.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.843][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.844][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.847][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.882][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.883][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.886][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:53.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.902][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:53.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:53.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.907][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:53.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:53.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.912][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:53.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:53.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.917][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:53.918][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:53.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.920][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.922][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:53.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:53.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.937][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.942][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.947][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.952][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.953][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.955][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.957][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:53.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.972][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.977][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.982][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.987][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.988][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.990][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:53.991][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:53.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:53.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.006][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.011][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.016][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.023][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.025][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.061][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.062][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.064][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.096][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.099][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.116][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.117][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.119][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.126][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.127][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.129][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.136][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.137][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.139][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.145][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.147][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.149][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.155][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.157][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.159][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.165][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.167][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.169][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.175][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.177][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.179][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.185][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.187][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.189][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.195][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.197][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.199][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.205][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:54.211][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:54.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.214][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.220][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.222][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.224][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.230][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-7799-content.xml".
biodb.DEBUG[2025-11-22 16:02:54.232][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:02:54.233][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-11-22 16:02:54.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:54.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:54.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:54.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:54.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:54.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:54.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:02:54.250][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.251][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.253][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.260][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.261][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.263][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.265][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.270][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.271][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.273][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.281][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.284][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.290][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.292][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.294][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.300][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.302][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.304][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.306][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.311][ef$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:54.312][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.314][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.316][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:02:54.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.321][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.322][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.325][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.331][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:54.333][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:54.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.335][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:54.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.342][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:02:54.343][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.345][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.347][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:02:54.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.352][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.353][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.356][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.357][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:54.418][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 7799.
biodb.TRACE[2025-11-22 16:02:54.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.450][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:02:54.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:02:54.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:02:54.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:02:54.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:02:54.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:02:54.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.465][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:02:54.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:02:54.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:54.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.566][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.570][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.586][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.591][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.601][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.602][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.605][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.606][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:54.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:54.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.636][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.638][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.640][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.672][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.673][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.675][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:54.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.692][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.697][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.702][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.707][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.708][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.710][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:54.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.745][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.746][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.749][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:54.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.779][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.781][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.783][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:54.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.799][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.804][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.813][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.815][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.817][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.818][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.833][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.838][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.843][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.849][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.850][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.853][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.854][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:54.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:54.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:54.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:54.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:54.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:54.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:54.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.891][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:54.893][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:54.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.895][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:54.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:54.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.936][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.937][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.939][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.941][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.960][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:54.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:54.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.964][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.970][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:02:54.972][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:02:54.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.974][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.981][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:54.982][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:54.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.985][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:54.991][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:54.994][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:54.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:54.997][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:55.003][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:55.005][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:55.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:55.007][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:55.023][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:55.025][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:55.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:55.034][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:55.045][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:55.046][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:02:55.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:55.049][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:55.055][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:55.059][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:55.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:55.061][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:55.067][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:02:55.069][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:02:55.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:55.071][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:55.077][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:55.079][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:55.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:55.081][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:55.087][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:55.089][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:55.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:55.091][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:02:55.101][biodb::testThat]
biodb.INFO [2025-11-22 16:02:55.106][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-22 16:02:55.107][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:55.109][biodb::testThat]
biodb.DEBUG[2025-11-22 16:02:55.111][private$loadEntries] Creating entries from ids [3]: "15440, 2528, 7799".
biodb.DEBUG[2025-11-22 16:02:55.202][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
fscache.INFO [2025-11-22 16:02:55.207][cch$loadContents] Load 3 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
biodb.DEBUG[2025-11-22 16:02:55.209][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:02:55.210][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-11-22 16:02:55.211][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:02:55.213][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-11-22 16:02:55.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:55.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:55.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:55.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:55.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:55.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:55.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-11-22 16:02:55.234][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
fscache.INFO [2025-11-22 16:02:55.261][private$cache$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/sched.
sched.DEBUG[2025-11-22 16:02:55.263][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:55.264][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:55.266][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:02:55.640][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:02:55.641][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:55.643][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:55.644][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:02:56.032][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:56.034][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:56.035][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:56.036][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:02:56.403][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:02:56.405][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:56.406][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:56.407][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:02:56.785][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:56.787][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:56.788][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:56.790][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:02:57.155][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:02:57.156][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:57.157][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:57.159][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:02:57.787][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:57.788][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:57.789][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:57.791][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:02:58.159][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:02:58.160][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:58.161][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:58.163][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:02:58.540][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:58.541][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:58.543][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:58.544][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:02:58.910][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:02:58.911][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:58.912][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:58.913][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:02:59.290][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:59.291][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:59.292][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:59.294][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:02:59.660][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:02:59.661][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:59.663][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:59.664][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:03:00.043][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:00.044][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:00.045][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:00.047][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:03:00.411][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:03:00.412][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:00.414][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:00.415][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:03:00.792][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:00.793][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:00.795][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:00.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:03:01.163][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:03:01.164][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:01.165][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:01.167][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:03:01.543][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:01.550][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:01.561][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:01.563][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:03:01.928][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:03:01.929][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:01.931][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:01.932][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:03:02.310][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:02.311][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:02.312][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:02.314][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:03:02.681][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:03:02.682][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:02.683][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:02.685][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:03:03.061][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
biodb.DEBUG[2025-11-22 16:03:03.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:03.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:03.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:03.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:03.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:03.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:03.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-11-22 16:03:03.098][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
fscache.INFO [2025-11-22 16:03:03.140][private$cache$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/sched.
sched.DEBUG[2025-11-22 16:03:03.161][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:03.163][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:03.164][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:03.533][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:03.535][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:03.536][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:03.537][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:03.913][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:03.915][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:03.916][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:03.918][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:04.284][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:04.285][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:04.296][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:04.297][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:04.675][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:04.676][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:04.677][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:04.679][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:05.044][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:05.045][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:05.047][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:05.048][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:05.657][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:05.659][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:05.660][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:05.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:06.027][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:06.029][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:06.032][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:06.033][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:06.699][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:06.701][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:06.702][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:06.703][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:07.069][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:07.071][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:07.074][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:07.078][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:07.459][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:07.460][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:07.461][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:07.463][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:07.832][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:07.833][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:07.835][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:07.836][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:08.448][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:08.449][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:08.450][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:08.452][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:08.817][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:08.818][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:08.819][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:08.820][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:09.197][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:09.199][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:09.200][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:09.202][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:09.566][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:09.567][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:09.569][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:09.570][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:09.947][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:09.948][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:09.949][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:09.951][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:10.317][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:10.318][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:10.319][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:10.320][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:16.846][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:16.847][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:16.849][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:16.850][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:03:17.216][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:03:17.217][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:17.219][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:17.222][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:03:17.843][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
biodb.DEBUG[2025-11-22 16:03:17.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:17.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:17.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:17.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:17.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:17.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:17.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-11-22 16:03:17.858][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
fscache.INFO [2025-11-22 16:03:17.860][private$cache$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/sched.
sched.DEBUG[2025-11-22 16:03:17.862][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:17.863][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:17.865][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:18.229][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:18.231][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:18.232][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:18.233][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:18.790][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:18.791][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:18.792][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:18.794][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:19.160][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:19.161][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:19.162][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:19.163][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:19.542][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:19.543][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:19.545][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:19.546][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:19.912][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:19.913][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:19.915][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:19.916][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:20.294][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:20.296][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:20.297][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:20.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:20.663][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:20.665][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:20.666][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:20.667][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:21.046][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:21.047][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:21.049][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:21.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:21.435][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:21.437][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:21.438][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:21.439][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:21.818][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:21.819][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:21.820][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:21.822][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:22.188][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:22.190][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:22.191][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:22.192][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:22.569][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:22.570][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:22.572][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:22.573][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:22.939][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:22.940][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:22.942][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:22.943][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:23.320][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:23.321][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:23.322][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:23.324][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:23.690][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:23.692][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:23.693][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:23.694][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:24.073][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:24.074][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:24.075][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:24.077][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:24.442][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:24.443][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:24.444][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:24.446][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:25.126][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:03:25.128][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:03:25.129][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:03:25.131][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:03:25.498][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:03:25.500][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:03:25.501][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:03:25.502][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:03:25.879][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
fscache.INFO [2025-11-22 16:03:25.881][cch$saveContents] Save 3 contents to /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
biodb.DEBUG[2025-11-22 16:03:25.883][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-11-22 16:03:25.884][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-11-22 16:03:25.886][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-11-22 16:03:25.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:25.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:25.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:25.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:25.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:25.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:25.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:25.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:25.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:25.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:25.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:25.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:25.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:25.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:25.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:25.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:25.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:25.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:25.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:25.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:25.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:25.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:25.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:25.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:25.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:03:25.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:25.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:25.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:25.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:25.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:25.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:03:25.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:25.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:03:25.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:25.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:25.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:25.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:25.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:25.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:25.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:26.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:03:26.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:03:26.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:26.097][self$createEntryFromContent] Accession numbers: NA, NA, NA.
biodb.DEBUG[2025-11-22 16:03:26.098][self$createEntryFromContent] Found 3 entry/ies without an accession number. Set it/them to NULL.
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:26.277][biodb::testThat]
biodb.INFO [2025-11-22 16:03:26.278][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-22 16:03:26.279][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:26.280][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:26.284][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:26.286][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:26.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:26.288][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:03:26.290][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
Saving _problems/test_long_100_generic-18.R
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:26.641][biodb::testThat]
biodb.INFO [2025-11-22 16:03:26.642][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-22 16:03:26.644][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:26.645][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:26.935][biodb::testThat]
biodb.INFO [2025-11-22 16:03:26.937][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-22 16:03:26.939][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:26.941][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:27.120][biodb::testThat]
biodb.INFO [2025-11-22 16:03:27.121][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-22 16:03:27.123][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:27.124][biodb::testThat]
biodb.INFO [2025-11-22 16:03:27.137][biodb::testThat]
biodb.INFO [2025-11-22 16:03:27.139][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-22 16:03:27.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:27.142][biodb::testThat]
biodb.INFO [2025-11-22 16:03:27.153][biodb::testThat]
biodb.INFO [2025-11-22 16:03:27.155][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:27.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:27.158][biodb::testThat]
biodb.DEBUG[2025-11-22 16:03:27.164][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
sched.TRACE[2025-11-22 16:03:27.719][try_get_rcurl_content] Using RCurl package for sending request (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440).
biodb.INFO [2025-11-22 16:03:28.106][biodb::testThat]
biodb.INFO [2025-11-22 16:03:28.107][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-22 16:03:28.108][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:28.110][biodb::testThat]
biodb.TRACE[2025-11-22 16:03:28.144][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:28.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:28.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:28.148][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:28.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:28.152][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:28.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:28.154][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:03:28.157][biodb::testThat]
biodb.INFO [2025-11-22 16:03:28.158][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-11-22 16:03:28.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:28.161][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:28.334][biodb::testThat]
biodb.INFO [2025-11-22 16:03:28.335][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-11-22 16:03:28.336][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:28.337][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:28.395][biodb::testThat]
biodb.INFO [2025-11-22 16:03:28.397][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-11-22 16:03:28.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:28.399][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:28.458][biodb::testThat]
biodb.INFO [2025-11-22 16:03:28.460][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-11-22 16:03:28.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:28.462][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.TRACE[2025-11-22 16:03:28.522][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:03:28.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:03:28.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:28.526][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:03:28.527][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:28.528][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:03:28.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:03:28.531][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:03:28.533][biodb::testThat]
biodb.INFO [2025-11-22 16:03:28.534][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-11-22 16:03:28.535][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:28.536][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:28.594][biodb::testThat]
biodb.INFO [2025-11-22 16:03:28.596][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-11-22 16:03:28.597][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:03:28.598][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:03:28.658][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:03:28.659][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-11-22 16:03:28.661][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:03:28.662][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:03:28.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:03:28.664][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:03:28.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:03:28.667][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:03:28.668][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".
[ FAIL 14 | WARN 0 | SKIP 1 | PASS 220 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:17:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label)
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_long_100_generic.R:17:1'): We can search for an entry by searchable field ──
Expected `!is.null(entry)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:17:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
── Failure ('test_long_100_generic.R:17:1'): We can search for an entry by name. ──
Expected `!is.null(entry)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:17:1'): We can search for an entry by name. ──
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
── Failure ('test_long_100_generic.R:17:1'): We can load an entry from the database. ──
Expected `any(vapply(entries, is.null, FUN.VALUE = TRUE))` to be FALSE.
Differences:
`actual`:   TRUE 
`expected`: FALSE

Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_100_generic.R:17:1'): We can load an entry from the database. ──
Expected `e` to inherit from "character".
Actual inheritance: "NULL"
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure ('test_long_100_generic.R:17:1'): We can search for a compound ──────
Expected `!is.null(entry)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:17:1'): We can search for a compound ────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
── Error ('test_long_100_generic.R:17:1'): annotateMzValues() accepts a single vector. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:17:1'): ppm tolerance works in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:17:1'): Input data frame is not modified by annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:17:1'): annotateMzValues() works correctly with real values. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:17:1'): Additional fields are accepted in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)

[ FAIL 14 | WARN 0 | SKIP 1 | PASS 220 ]
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 biodbChebi_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbChebi.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* 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 ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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:
   3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
   4.     └─biodb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:17:1'): Additional fields are accepted in annotateMzValues() ──
  Error in `e$hasField(mf)`: attempt to apply non-function
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
   3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
   4.     └─biodb (local) FUN(X[[i]], ...)
  
  [ FAIL 14 | WARN 0 | SKIP 1 | PASS 220 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbChebi.Rcheck/00install.out

* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.16.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)