Back to Long Tests report for BioC 3.20

This page was generated on 2025-01-25 23:55 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
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 8/32HostnameOS / ArchCHECK
biodbHmdb 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-01-25 09:55 -0500 (Sat, 25 Jan 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_20
git_last_commit: 0eb718c
git_last_commit_date: 2024-10-29 11:06:39 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  WARNINGS  
merida1macOS 12.7.5 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on palomino8

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

raw results


Summary

Package: biodbHmdb
Version: 1.12.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.12.0.tar.gz
StartedAt: 2025-01-25 16:02:50 -0500 (Sat, 25 Jan 2025)
EndedAt: 2025-01-25 16:04:58 -0500 (Sat, 25 Jan 2025)
EllapsedTime: 128.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 2

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-01-25 16:04:25.357][biodb::testContext]
biodb.INFO [2025-01-25 16:04:25.360][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:04:25.361][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-25 16:04:25.363][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:04:25.364][biodb::testContext]
biodb.INFO [2025-01-25 16:04:25.370][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:04:25.372][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-25 16:04:25.380][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:04:25.381][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-25 16:04:25.383][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-25 16:04:25.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.387][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-25 16:04:25.403][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-25 16:04:25.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.406][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.407][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-25 16:04:25.409][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-25 16:04:25.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.413][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-25 16:04:25.414][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-25 16:04:25.416][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-25 16:04:25.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.419][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.420][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-25 16:04:25.421][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-25 16:04:25.423][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-25 16:04:25.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.427][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-25 16:04:25.428][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-25 16:04:25.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.431][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.433][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-25 16:04:25.434][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-25 16:04:25.435][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-25 16:04:25.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.439][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-25 16:04:25.441][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-25 16:04:25.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.444][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.445][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-25 16:04:25.446][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-25 16:04:25.447][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-25 16:04:25.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.452][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:04:25.453][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-25 16:04:25.454][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-25 16:04:25.455][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-25 16:04:25.457][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-25 16:04:25.458][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-25 16:04:25.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.461][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.462][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-25 16:04:25.463][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-25 16:04:25.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.468][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-25 16:04:25.469][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-25 16:04:25.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.472][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.473][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-25 16:04:25.475][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-25 16:04:25.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.479][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-25 16:04:25.480][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:04:25.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.483][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.485][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-25 16:04:25.486][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-25 16:04:25.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.490][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:04:25.491][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-25 16:04:25.495][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-25 16:04:25.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.498][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.500][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-25 16:04:25.501][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-25 16:04:25.502][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-25 16:04:25.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.508][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-25 16:04:25.544][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.558][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-25 16:04:25.559][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.561][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:04:25.562][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.563][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.564][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.565][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.567][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:04:25.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:04:25.569][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.570][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-25 16:04:25.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:04:25.573][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.574][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.575][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:04:25.575][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:04:25.575][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:04:25.575][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:04:25.575][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:04:25.577][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:04:25.578][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:25.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:25.580][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:04:25.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:25.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:25.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.585][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.586][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:04:25.587][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:04:25.588][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.589][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.591][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-25 16:04:25.593][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.594][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:04:25.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.596][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:04:25.597][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.599][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.600][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.601][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.602][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:04:25.604][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:04:25.605][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.606][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-25 16:04:25.607][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:04:25.608][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.610][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.611][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:04:25.611][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:04:25.611][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:04:25.611][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:04:25.611][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:04:25.612][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:04:25.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:25.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:25.615][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:04:25.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:25.618][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:25.619][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.620][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.621][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:04:25.622][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:04:25.623][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.625][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.626][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-25 16:04:25.628][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.629][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-25 16:04:25.630][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.632][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:04:25.633][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.635][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.636][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.638][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:04:25.639][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:04:25.640][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.641][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-25 16:04:25.642][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:04:25.644][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.645][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.646][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.647][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:04:25.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:25.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:25.651][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:04:25.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:25.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:25.654][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.655][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.656][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:04:25.658][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:04:25.659][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.660][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.661][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-25 16:04:25.663][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.664][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:04:25.666][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.667][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:04:25.668][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.669][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.671][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.672][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.673][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:04:25.674][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:04:25.675][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.677][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-25 16:04:25.678][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:04:25.679][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.680][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:25.681][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.683][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:04:25.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:25.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:25.686][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:04:25.687][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:25.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:25.689][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:04:25.691][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:04:25.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:04:25.694][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:25.695][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:25.699][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:04:25.700][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.701][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.706][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.712][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.717][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.723][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.728][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.734][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.739][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.750][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.777][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.788][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.794][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.799][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.800][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-25 16:04:25.805][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-25 16:04:25.806][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-25 16:04:25.808][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-25 16:04:25.809][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-25 16:04:25.811][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:04:25.813][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-25 16:04:25.814][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-25 16:04:25.816][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-25 16:04:25.817][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:04:25.819][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:04:25.820][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-25 16:04:25.822][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-25 16:04:25.824][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-25 16:04:25.825][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-25 16:04:25.827][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:04:25.828][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-25 16:04:25.830][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-25 16:04:25.831][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-25 16:04:25.833][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-25 16:04:25.835][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-25 16:04:25.836][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-25 16:04:25.838][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-25 16:04:25.839][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-25 16:04:25.841][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-25 16:04:25.843][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-25 16:04:25.844][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-25 16:04:25.846][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-25 16:04:25.847][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-25 16:04:25.849][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-25 16:04:25.851][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-25 16:04:25.852][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-25 16:04:25.854][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-25 16:04:25.855][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-25 16:04:25.857][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-25 16:04:25.858][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-25 16:04:25.860][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-25 16:04:25.862][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-25 16:04:25.863][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-25 16:04:25.865][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-25 16:04:25.866][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-25 16:04:25.868][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-25 16:04:25.870][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-25 16:04:25.871][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-25 16:04:25.873][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-25 16:04:25.874][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-25 16:04:25.876][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-25 16:04:25.878][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-25 16:04:25.879][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-25 16:04:25.881][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-25 16:04:25.882][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-25 16:04:25.884][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-25 16:04:25.886][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-25 16:04:25.887][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-25 16:04:25.889][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-25 16:04:25.890][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-25 16:04:25.892][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-25 16:04:25.894][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-25 16:04:25.895][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-25 16:04:25.897][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-25 16:04:25.898][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-25 16:04:25.900][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-25 16:04:25.902][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-25 16:04:25.903][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-25 16:04:25.905][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-25 16:04:25.906][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-25 16:04:25.908][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-25 16:04:25.910][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-25 16:04:25.911][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-25 16:04:25.913][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-25 16:04:25.914][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-25 16:04:25.916][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-25 16:04:25.917][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-25 16:04:25.919][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-25 16:04:25.921][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-25 16:04:25.922][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-25 16:04:25.924][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-25 16:04:25.925][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-25 16:04:25.927][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-25 16:04:25.929][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-25 16:04:25.930][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-25 16:04:25.932][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-25 16:04:25.933][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-25 16:04:25.967][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-25 16:04:25.970][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:04:25.973][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:04:25.974][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.976][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.977][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:25.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:25.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:25.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:25.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:25.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:25.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:25.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:25.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:25.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:25.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.003][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:26.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.018][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.025][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.033][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.041][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.048][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.055][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.063][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.071][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.078][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.086][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.105][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.117][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.125][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:26.134][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:04:26.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:04:26.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:04:26.145][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-25 16:04:26.154][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:04:26.156][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:26.157][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-25 16:04:26.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:26.159][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:04:26.160][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:26.162][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-25 16:04:26.163][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:26.164][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:04:26.165][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-25 16:04:26.166][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:04:26.168][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:26.169][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-25 16:04:26.170][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-25 16:04:26.171][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-25 16:04:26.173][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-25 16:04:26.174][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:04:26.174][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-25 16:04:26.174][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-25 16:04:26.175][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-25 16:04:26.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:26.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:26.178][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:04:26.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:04:26.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:04:26.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:04:26.183][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-25 16:04:26.183][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-25 16:04:26.184][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:04:26.185][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:04:26.186][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-25 16:04:26.188][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:04:26.193][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-25 16:04:26.195][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:04:26.197][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:04:26.199][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:04:26.200][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:04:26.253][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:04:26.256][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-25 16:04:26.262][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:04:26.269][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-25 16:04:26.275][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:04:26.277][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:04:26.280][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-25 16:04:26.282][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-01-25 16:04:26.293][biodb::testThat]
biodb.INFO [2025-01-25 16:04:26.295][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-25 16:04:26.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:26.297][biodb::testThat]
biodb.TRACE[2025-01-25 16:04:26.303][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-01-25 16:04:26.305][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:04:26.309][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-25 16:04:26.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:04:26.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:26.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:26.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:26.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:26.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:26.337][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:04:26.348][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.350][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.352][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.369][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.370][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.373][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.395][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.400][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.402][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.404][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.406][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.411][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.412][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.414][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.416][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.421][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.422][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.424][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.431][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.432][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.435][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.441][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.443][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.445][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.446][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.451][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.453][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.455][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.467][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.472][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.473][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.475][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.477][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.482][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.483][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.486][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.492][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:26.493][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:26.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.496][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.497][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:26.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:26.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.502][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:26.503][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:26.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.506][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:26.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:26.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.512][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.514][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.516][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.522][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.524][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.526][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.533][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.534][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.536][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.542][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:26.544][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:26.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.546][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.547][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:26.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:26.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.552][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:26.554][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:26.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.556][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.558][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:26.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:26.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.563][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:04:26.564][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:26.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.566][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.568][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:04:26.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:26.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.614][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.619][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.629][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:26.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.634][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.638][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.643][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:26.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:26.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:26.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.677][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.686][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:26.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.701][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:26.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:26.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:26.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:26.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:26.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:26.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:26.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.720][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:26.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:26.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.725][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:26.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:26.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.730][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:26.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:26.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:26.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:26.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:26.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:26.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:26.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:26.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:26.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:26.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:26.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:26.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:26.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:26.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.778][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.782][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.787][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:26.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:26.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.826][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.831][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.836][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:26.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.840][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.845][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.850][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:26.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.855][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:26.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:26.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.860][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:26.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:26.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.864][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:26.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:26.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.869][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:04:26.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.889][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:04:26.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:26.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.928][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:26.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:26.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.933][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:26.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:26.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.938][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:26.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:26.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.948][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:26.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:26.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:26.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:26.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:26.987][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-25 16:04:26.990][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:04:26.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:04:26.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:26.995][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:04:26.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:04:26.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:26.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.000][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:04:27.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:04:27.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.005][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:04:27.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:04:27.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.048][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:27.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:27.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.090][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:27.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:27.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.095][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:27.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:27.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.100][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:27.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:27.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.128][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.132][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.147][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.152][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.157][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.162][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.163][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.166][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.172][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.202][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.203][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.205][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.221][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.226][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.238][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.239][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.241][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.243][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.272][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.273][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.276][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.291][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.296][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.301][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.306][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.307][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.310][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.311][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:27.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:27.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:27.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:27.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:27.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:27.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.340][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:27.341][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:27.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.344][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:27.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:27.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.364][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:27.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:27.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.369][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:27.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:27.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.374][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:27.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:27.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.379][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:27.380][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:27.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.382][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.384][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:27.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:27.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.398][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:27.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:27.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:27.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:27.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:27.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:27.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.412][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:27.414][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:27.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.416][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.417][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:27.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:27.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.432][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.436][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.441][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.446][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.447][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.449][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.451][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.482][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.483][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.486][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.507][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.512][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.516][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.518][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.520][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.535][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.555][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.556][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.559][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.560][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.575][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.580][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.590][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.591][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.593][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.594][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:27.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:27.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:27.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:27.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.618][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:27.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:27.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:27.624][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:27.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.627][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.628][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:27.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:27.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:27.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:27.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.647][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:27.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:27.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:27.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:27.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.656][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:27.658][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:27.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.660][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:27.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:27.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.690][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.691][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.693][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.708][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.713][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.718][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.723][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.729][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.731][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.733][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.747][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:27.748][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:27.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.751][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.757][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.758][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:27.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.761][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.767][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.768][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:27.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.770][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.777][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.778][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:27.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.780][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.786][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.788][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:27.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.790][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.796][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.797][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:27.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.799][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.806][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.807][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:27.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.809][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.815][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.817][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:27.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.819][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.825][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:27.826][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:27.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.829][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.835][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:27.836][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:27.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.838][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.844][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:27.846][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:27.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.848][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.854][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.855][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:27.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.857][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.863][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.865][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:27.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.867][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.873][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.874][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:27.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.876][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.883][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:27.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:27.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.886][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.892][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.893][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:27.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.896][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.902][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.903][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:27.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.906][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:27.912][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:27.913][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:27.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:27.916][ef$get] fields variable is a list.
biodb.INFO [2025-01-25 16:04:27.933][biodb::testThat]
biodb.INFO [2025-01-25 16:04:27.934][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-25 16:04:27.935][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:27.937][biodb::testThat]
biodb.DEBUG[2025-01-25 16:04:27.950][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-25 16:04:27.957][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-25 16:04:27.964][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:27.966][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-25 16:04:27.969][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-01-25 16:04:27.971][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-25 16:04:27.987][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-01-25 16:04:27.989][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-25 16:04:28.010][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:04:28.012][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-25 16:04:28.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:04:28.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:28.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:28.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:28.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:28.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:28.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-25 16:04:28.031][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.032][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.035][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.041][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.042][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.045][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.046][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.052][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.053][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.055][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.057][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.062][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.063][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.066][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.067][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.072][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.073][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.076][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.082][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.084][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.086][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.093][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.094][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.096][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.098][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.103][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.104][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.106][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.108][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.119][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.120][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.122][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.124][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.129][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.130][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.133][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.139][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:28.141][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:28.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.143][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.144][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:28.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:28.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.149][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:28.151][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:28.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.153][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:28.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:28.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.159][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.161][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.163][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.169][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.171][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.173][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.180][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.181][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.183][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.190][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.191][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.193][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.200][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:28.201][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:28.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.203][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:28.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:28.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.210][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:04:28.211][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:28.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.213][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.215][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:04:28.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:28.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.235][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.240][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.245][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:04:28.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.250][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.255][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.260][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:04:28.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:04:28.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:04:28.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.299][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.303][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:04:28.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.313][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.318][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.323][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:04:28.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.328][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:28.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:28.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:28.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:28.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:28.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:04:28.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.342][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.347][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.351][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:28.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:28.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.361][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:28.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:28.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.366][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:04:28.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:04:28.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:28.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:28.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:28.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:28.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:04:28.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:04:28.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.399][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.404][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.408][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:04:28.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:04:28.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.428][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.442][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.447][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.451][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:04:28.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.456][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.466][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.471][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.475][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:28.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:28.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:28.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:28.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.485][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:04:28.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:04:28.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.490][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:04:28.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.509][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:04:28.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:04:28.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.539][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:28.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:28.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.543][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:28.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:28.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.553][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:28.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:04:28.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:04:28.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:04:28.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.586][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-25 16:04:28.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-25 16:04:28.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-25 16:04:28.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:04:28.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:04:28.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:04:28.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:04:28.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-25 16:04:28.612][biodb::testThat]
biodb.INFO [2025-01-25 16:04:28.613][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-25 16:04:28.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:28.615][biodb::testThat]
biodb.TRACE[2025-01-25 16:04:28.619][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.622][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.624][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-01-25 16:04:28.657][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.675][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-01-25 16:04:28.676][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-25 16:04:28.677][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-25 16:04:28.678][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-25 16:04:28.681][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.682][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.684][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-25 16:04:28.686][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.687][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-25 16:04:28.689][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-25 16:04:28.690][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-25 16:04:28.691][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-25 16:04:28.693][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-25 16:04:28.694][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-25 16:04:28.695][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-25 16:04:28.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:28.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:28.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.716][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-25 16:04:28.717][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-25 16:04:28.718][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-25 16:04:28.735][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.737][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.739][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.741][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-01-25 16:04:28.758][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.768][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.775][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2025-01-25 16:04:28.825][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-25 16:04:28.827][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-01-25 16:04:28.828][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-01-25 16:04:28.840][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.842][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.844][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-25 16:04:28.846][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.847][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-25 16:04:28.860][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-25 16:04:28.861][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-25 16:04:28.862][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-25 16:04:28.864][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-25 16:04:28.865][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-25 16:04:28.866][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-25 16:04:28.868][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.876][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.881][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.886][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:28.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:28.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.891][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-25 16:04:28.892][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-25 16:04:28.893][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-25 16:04:28.910][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.911][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.914][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.915][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-01-25 16:04:28.932][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.942][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.947][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.955][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-01-25 16:04:28.956][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-01-25 16:04:28.957][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-25 16:04:28.959][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-25 16:04:28.961][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.963][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.964][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-25 16:04:28.966][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:28.967][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-25 16:04:28.969][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-25 16:04:28.970][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-25 16:04:28.972][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-25 16:04:28.973][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-25 16:04:28.974][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-25 16:04:28.975][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-25 16:04:28.978][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.983][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.988][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:28.992][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:28.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:28.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:28.997][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-25 16:04:28.998][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-25 16:04:29.000][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-01-25 16:04:29.021][biodb::testThat]
biodb.INFO [2025-01-25 16:04:29.023][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-25 16:04:29.024][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:29.025][biodb::testThat]
biodb.TRACE[2025-01-25 16:04:29.040][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:29.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:29.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:29.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:29.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:29.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:29.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:29.067][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-25 16:04:29.068][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-25 16:04:29.069][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-25 16:04:29.071][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:29.073][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:29.075][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-25 16:04:29.077][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:04:29.078][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-25 16:04:29.080][private$doListFiles] List files in C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-25 16:04:29.081][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-25 16:04:29.082][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-25 16:04:29.083][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-25 16:04:29.085][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-25 16:04:29.086][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-25 16:04:29.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:29.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:29.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:29.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:29.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:29.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:29.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:29.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:04:29.108][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-25 16:04:29.109][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-01-25 16:04:29.137][biodb::testThat]
biodb.INFO [2025-01-25 16:04:29.138][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-25 16:04:29.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:29.141][biodb::testThat]
biodb.TRACE[2025-01-25 16:04:29.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:04:29.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:04:29.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:04:29.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:04:29.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.173][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:04:29.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:04:29.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:04:29.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:04:29.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.217][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:04:29.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:04:29.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.223][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:04:29.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:04:29.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.228][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:04:29.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:04:29.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:29.232][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:04:29.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:04:29.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:29.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-25 16:04:29.245][biodb::testThat]
biodb.INFO [2025-01-25 16:04:29.247][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-25 16:04:29.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:29.249][biodb::testThat]
biodb.INFO [2025-01-25 16:04:29.260][biodb::testThat]
biodb.INFO [2025-01-25 16:04:29.261][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-25 16:04:29.262][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:29.263][biodb::testThat]
biodb.INFO [2025-01-25 16:04:29.274][biodb::testThat]
biodb.INFO [2025-01-25 16:04:29.280][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-25 16:04:29.281][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:29.283][biodb::testThat]
biodb.DEBUG[2025-01-25 16:04:29.287][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-01-25 16:04:32.008][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-01-25 16:04:48.611][biodb::testThat]
biodb.INFO [2025-01-25 16:04:48.612][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-25 16:04:48.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:04:48.615][biodb::testThat]
biodb.DEBUG[2025-01-25 16:04:48.768][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-01-25 16:04:57.273][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:57.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:57.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:57.277][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:57.278][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:57.280][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:57.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:57.282][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:57.283][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:57.285][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:57.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:57.287][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:57.288][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:04:57.290][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:04:57.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:57.292][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:57.293][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:04:57.295][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:04:57.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:57.297][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:04:57.298][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:57.299][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:04:57.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:04:57.302][ef$get] fields variable is a list.
biodb.INFO [2025-01-25 16:04:57.303][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-25 16:04:57.304][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-25 16:04:57.306][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-25 16:04:57.307][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-25 16:04:57.308][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:04:57.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:04:57.310][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:04:57.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:04:57.312][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:04:57.313][FUN] Functions in observer 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 0 | WARN 0 | SKIP 0 | PASS 147 ]
> 
> proc.time()
   user  system elapsed 
   5.62    0.43   33.81

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbHmdb/DESCRIPTION' ... OK
* this is package 'biodbHmdb' version '1.12.0'
* 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 whether package 'biodbHmdb' can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'zip'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'HmdbMetabolitesConn' 'HmdbMetabolitesEntry' 'hmdbToSqlite'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log'
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package 'biodbHmdb' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor 'EntryMaker::EntryMaker()':
EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbHmdb.dll tmp.def EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'biodbHmdb' 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)