Back to Long Tests report for BioC 3.20

This page was generated on 2024-09-21 23:55 -0400 (Sat, 21 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4438
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4451
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4484
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 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-09-21 09:55 -0400 (Sat, 21 Sep 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: c3d59a4
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on lconway

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

raw results


Summary

Package: biodbHmdb
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.11.0.tar.gz
StartedAt: 2024-09-21 16:01:06 -0400 (Sat, 21 Sep 2024)
EndedAt: 2024-09-21 16:02:39 -0400 (Sat, 21 Sep 2024)
EllapsedTime: 92.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 1

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-09-21 16:02:02.519][biodb::testContext]
biodb.INFO [2024-09-21 16:02:02.522][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-21 16:02:02.523][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-09-21 16:02:02.523][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-21 16:02:02.524][biodb::testContext]
biodb.INFO [2024-09-21 16:02:02.529][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-21 16:02:02.531][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-09-21 16:02:02.537][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-21 16:02:02.537][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-21 16:02:02.538][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-21 16:02:02.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.541][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-21 16:02:02.554][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-21 16:02:02.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.556][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.557][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-21 16:02:02.558][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-21 16:02:02.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.560][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-21 16:02:02.561][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-21 16:02:02.562][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-21 16:02:02.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.564][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.564][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-21 16:02:02.565][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-21 16:02:02.566][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-21 16:02:02.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.569][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-21 16:02:02.570][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-21 16:02:02.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.573][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-21 16:02:02.573][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-21 16:02:02.574][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-21 16:02:02.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.577][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-21 16:02:02.578][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-21 16:02:02.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.580][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.580][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-21 16:02:02.581][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-21 16:02:02.582][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-21 16:02:02.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.585][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-21 16:02:02.585][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-21 16:02:02.586][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-21 16:02:02.587][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-21 16:02:02.588][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-21 16:02:02.589][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-21 16:02:02.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.591][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.591][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-21 16:02:02.592][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-21 16:02:02.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.595][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-21 16:02:02.596][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-21 16:02:02.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.597][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.598][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-21 16:02:02.599][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-21 16:02:02.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.602][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-21 16:02:02.602][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-21 16:02:02.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.604][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.605][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-21 16:02:02.606][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-21 16:02:02.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.609][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-21 16:02:02.609][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-21 16:02:02.626][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-21 16:02:02.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.629][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-21 16:02:02.630][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-21 16:02:02.631][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-21 16:02:02.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.636][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-21 16:02:02.660][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.675][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-21 16:02:02.676][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.677][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:02:02.678][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.678][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.679][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.680][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.681][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-21 16:02:02.681][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:02:02.682][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.683][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-21 16:02:02.683][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:02:02.684][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.685][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.686][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-21 16:02:02.686][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-21 16:02:02.686][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-21 16:02:02.686][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-21 16:02:02.686][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-21 16:02:02.687][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-21 16:02:02.687][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:02.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:02.689][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:02:02.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:02.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:02.691][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.691][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:02:02.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:02:02.693][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.694][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.695][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-21 16:02:02.696][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.697][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-21 16:02:02.698][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.698][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:02:02.699][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.700][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.701][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.701][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.702][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-21 16:02:02.703][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:02:02.704][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.705][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-21 16:02:02.705][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:02:02.706][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.707][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.707][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-21 16:02:02.707][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-21 16:02:02.707][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-21 16:02:02.707][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-21 16:02:02.707][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-21 16:02:02.708][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-21 16:02:02.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:02.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:02.710][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:02:02.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:02.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:02.712][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.713][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.714][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:02:02.714][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:02:02.715][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.716][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.717][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-21 16:02:02.718][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.719][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-21 16:02:02.719][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.720][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:02:02.721][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.722][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.722][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.723][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.724][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-21 16:02:02.725][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:02:02.725][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.726][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-21 16:02:02.727][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:02:02.728][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.728][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.729][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.730][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-21 16:02:02.730][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:02.731][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:02.732][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:02:02.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:02.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:02.734][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.734][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.735][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:02:02.736][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:02:02.736][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.737][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.738][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-21 16:02:02.739][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.740][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-21 16:02:02.741][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.741][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:02:02.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.743][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.743][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.744][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.745][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-21 16:02:02.746][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:02:02.746][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.747][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-21 16:02:02.748][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:02:02.748][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.749][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:02.750][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.751][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-21 16:02:02.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:02.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:02.753][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:02:02.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:02.754][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:02.755][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:02:02.756][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.757][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:02:02.757][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:02:02.758][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:02.759][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:02.762][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-21 16:02:02.763][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.773][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.776][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.780][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.783][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.795][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.802][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.805][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.811][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.814][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.818][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.821][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.822][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-21 16:02:02.826][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-21 16:02:02.827][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-21 16:02:02.828][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-21 16:02:02.829][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-21 16:02:02.830][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-21 16:02:02.831][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-21 16:02:02.832][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-21 16:02:02.833][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-21 16:02:02.834][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-21 16:02:02.835][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-21 16:02:02.836][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-21 16:02:02.837][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-21 16:02:02.838][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-21 16:02:02.839][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-21 16:02:02.840][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-21 16:02:02.841][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-21 16:02:02.842][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-21 16:02:02.843][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-21 16:02:02.844][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-21 16:02:02.845][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-21 16:02:02.846][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-21 16:02:02.847][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-21 16:02:02.848][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-21 16:02:02.849][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-21 16:02:02.851][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-21 16:02:02.852][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-21 16:02:02.853][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-21 16:02:02.854][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-21 16:02:02.855][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-21 16:02:02.856][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-21 16:02:02.857][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-21 16:02:02.858][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-21 16:02:02.859][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-21 16:02:02.860][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-21 16:02:02.861][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-21 16:02:02.862][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-21 16:02:02.863][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-21 16:02:02.864][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-21 16:02:02.866][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-21 16:02:02.867][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-21 16:02:02.868][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-21 16:02:02.869][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-21 16:02:02.870][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-21 16:02:02.871][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-21 16:02:02.872][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-21 16:02:02.873][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-21 16:02:02.874][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-21 16:02:02.875][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-21 16:02:02.876][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-21 16:02:02.878][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-21 16:02:02.879][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-21 16:02:02.880][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-21 16:02:02.881][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-21 16:02:02.882][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-21 16:02:02.883][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-21 16:02:02.884][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-21 16:02:02.885][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-21 16:02:02.886][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-21 16:02:02.887][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-21 16:02:02.888][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-21 16:02:02.889][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-21 16:02:02.890][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-21 16:02:02.891][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-21 16:02:02.892][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-21 16:02:02.893][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-21 16:02:02.894][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-21 16:02:02.895][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-21 16:02:02.896][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-21 16:02:02.897][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-21 16:02:02.898][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-21 16:02:02.899][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-21 16:02:02.900][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-21 16:02:02.901][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-21 16:02:02.902][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-21 16:02:02.903][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-21 16:02:02.904][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-21 16:02:02.905][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-21 16:02:02.906][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-21 16:02:02.907][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-21 16:02:02.908][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-21 16:02:02.909][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-21 16:02:02.910][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-21 16:02:02.914][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-21 16:02:02.916][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-21 16:02:02.918][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-21 16:02:02.918][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.920][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.920][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.928][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:02.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.942][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.947][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.977][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[2024-09-21 16:02:02.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.981][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.986][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.991][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:02.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:02.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:02.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:02.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:02.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:02.998][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:02.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.003][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[2024-09-21 16:02:03.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:03.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:03.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:03.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.022][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:03.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.027][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.DEBUG[2024-09-21 16:02:03.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:03.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.037][FUN] Functions in observer BiodbConfig: [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[2024-09-21 16:02:03.038][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-21 16:02:03.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:02:03.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:02:03.045][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-09-21 16:02:03.052][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-09-21 16:02:03.054][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:03.055][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-21 16:02:03.055][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:03.056][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:02:03.057][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:03.058][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-09-21 16:02:03.059][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:03.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:02:03.061][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-21 16:02:03.061][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:02:03.062][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:03.063][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-09-21 16:02:03.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-09-21 16:02:03.065][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-09-21 16:02:03.066][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-21 16:02:03.067][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-21 16:02:03.067][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-09-21 16:02:03.067][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-09-21 16:02:03.067][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-21 16:02:03.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:03.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:03.070][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:02:03.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:02:03.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:02:03.072][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:02:03.073][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-09-21 16:02:03.073][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-09-21 16:02:03.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:02:03.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:02:03.075][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-21 16:02:03.076][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:02:03.080][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-09-21 16:02:03.081][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-21 16:02:03.083][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-21 16:02:03.084][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-21 16:02:03.085][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-21 16:02:03.105][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-09-21 16:02:03.106][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-09-21 16:02:03.109][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-09-21 16:02:03.137][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-21 16:02:03.141][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-21 16:02:03.141][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-21 16:02:03.142][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-09-21 16:02:03.143][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-09-21 16:02:03.150][biodb::testThat]
biodb.INFO [2024-09-21 16:02:03.151][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-09-21 16:02:03.152][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:03.152][biodb::testThat]
biodb.TRACE[2024-09-21 16:02:03.155][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-09-21 16:02:03.157][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-21 16:02:03.159][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-21 16:02:03.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-21 16:02:03.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:03.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:03.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:03.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:03.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:03.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-21 16:02:03.189][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.190][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.191][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.204][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.205][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.206][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.224][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.227][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.228][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.229][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.230][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.233][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.234][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.235][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.236][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.242][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.245][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.246][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.248][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.252][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.252][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.254][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.255][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.258][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.258][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.260][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.261][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.264][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.264][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.266][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.267][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.276][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.276][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.278][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.281][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.282][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.283][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.288][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:03.288][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:03.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.290][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.291][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:03.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:03.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.294][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.295][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.297][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.302][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.303][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.307][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.308][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.309][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.310][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.313][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.314][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.315][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.316][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.319][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:03.320][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:03.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.322][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.323][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:03.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:03.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.326][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-21 16:02:03.327][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.328][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.329][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-21 16:02:03.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.363][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.367][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.370][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.373][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.376][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.383][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:03.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.403][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.406][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.409][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.416][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.419][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:03.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.422][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.425][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.431][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.435][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.438][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.441][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.444][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:03.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:03.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:03.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:03.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:03.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:03.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.469][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.473][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.476][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.502][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.505][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.508][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.511][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.515][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.529][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.533][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:03.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:03.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:03.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:03.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.540][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:03.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:03.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.543][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-21 16:02:03.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.555][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-21 16:02:03.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:03.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.587][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.591][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.597][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:03.618][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-09-21 16:02:03.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:02:03.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:02:03.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.623][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:02:03.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:02:03.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.630][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-21 16:02:03.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-21 16:02:03.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.633][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-21 16:02:03.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-21 16:02:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.662][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.690][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.693][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.696][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:03.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.714][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.715][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.716][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:03.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.728][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.730][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.734][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.737][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.738][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.739][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.740][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:03.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.763][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.764][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.766][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:03.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.777][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.779][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.782][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.786][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.786][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.788][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.788][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:03.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.808][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.809][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.810][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:03.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.821][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.824][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.827][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.830][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.831][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.832][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.833][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:03.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.852][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.853][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.855][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:03.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:03.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.865][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.868][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.871][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.874][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.875][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.877][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.881][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:03.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:03.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.900][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.901][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.902][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:03.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:03.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.913][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.916][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.920][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.923][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.924][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.925][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.926][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:03.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.944][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.945][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.947][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:03.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.958][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.961][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.967][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.967][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.969][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.970][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:03.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.979][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.985][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.988][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.989][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.990][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:03.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:03.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:03.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.008][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.010][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.014][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.014][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.016][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.017][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.032][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.035][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.036][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.037][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.038][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.057][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.058][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.060][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.080][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.081][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.083][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.093][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.097][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.103][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.103][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.105][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.106][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.115][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.116][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.117][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.122][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.122][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.128][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.132][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.133][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.134][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.138][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.139][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.140][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.144][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.145][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.146][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.153][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.154][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.155][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.159][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.160][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.161][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.166][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.167][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.168][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.172][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.173][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.174][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.179][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:04.180][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:04.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.181][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.185][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.187][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.191][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.192][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.193][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.197][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.198][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.199][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.204][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.204][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.206][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.210][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.211][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.212][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.222][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.223][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.225][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.229][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.230][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.231][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.235][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.236][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.237][ef$get] fields variable is a list.
biodb.INFO [2024-09-21 16:02:04.244][biodb::testThat]
biodb.INFO [2024-09-21 16:02:04.245][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-09-21 16:02:04.245][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:04.246][biodb::testThat]
biodb.DEBUG[2024-09-21 16:02:04.257][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-09-21 16:02:04.266][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-09-21 16:02:04.306][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:04.307][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-09-21 16:02:04.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-09-21 16:02:04.310][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-21 16:02:04.317][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-09-21 16:02:04.318][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-09-21 16:02:04.335][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-21 16:02:04.336][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-21 16:02:04.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-21 16:02:04.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:04.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:04.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:04.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:04.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:04.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-21 16:02:04.348][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.349][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.350][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.354][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.355][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.357][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.358][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.361][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.362][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.363][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.364][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.367][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.368][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.369][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.370][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.374][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.374][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.376][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.380][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.381][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.382][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.386][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.387][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.388][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.389][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.392][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.393][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.394][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.395][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.398][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.399][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.400][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.401][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.404][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.405][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.406][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.407][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.410][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:04.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:04.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.412][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.413][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:04.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:04.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.420][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.421][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.423][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.427][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.427][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.429][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.433][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.434][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.435][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.439][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.439][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.441][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.445][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.446][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.447][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.448][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.451][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.452][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.453][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.454][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.457][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-21 16:02:04.458][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.459][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.460][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-21 16:02:04.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.483][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.504][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.507][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:02:04.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.510][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.513][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.516][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:02:04.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:02:04.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:02:04.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.548][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.551][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.553][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:02:04.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.562][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:02:04.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.569][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.572][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.575][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:02:04.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.578][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.580][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.584][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.586][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:04.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:04.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.589][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:04.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:04.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.592][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:02:04.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:02:04.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:02:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:02:04.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.615][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.618][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:02:04.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:02:04.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.639][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.657][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.660][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:02:04.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.663][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.667][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.670][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:04.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.673][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.677][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.680][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:02:04.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:02:04.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.683][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-21 16:02:04.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.686][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.699][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-21 16:02:04.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:02:04.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:04.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:04.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.721][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:04.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:04.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.728][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:04.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:02:04.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:02:04.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:02:04.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:04.751][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-09-21 16:02:04.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-09-21 16:02:04.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-09-21 16:02:04.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-09-21 16:02:04.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-09-21 16:02:04.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-09-21 16:02:04.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-09-21 16:02:04.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-21 16:02:04.780][biodb::testThat]
biodb.INFO [2024-09-21 16:02:04.780][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-09-21 16:02:04.781][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:04.782][biodb::testThat]
biodb.TRACE[2024-09-21 16:02:04.784][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.785][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.787][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:04.788][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-09-21 16:02:04.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:04.830][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-09-21 16:02:04.831][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-09-21 16:02:04.832][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-09-21 16:02:04.833][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-09-21 16:02:04.834][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:04.835][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:04.836][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-21 16:02:04.838][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:04.838][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-21 16:02:04.839][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-21 16:02:04.840][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-21 16:02:04.842][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-21 16:02:04.843][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-21 16:02:04.843][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-21 16:02:04.844][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-21 16:02:04.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:04.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:04.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:04.859][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-21 16:02:04.860][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-21 16:02:04.861][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-09-21 16:02:04.877][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.878][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.880][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:04.881][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-09-21 16:02:04.898][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.902][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.905][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:04.911][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[2024-09-21 16:02:04.955][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-09-21 16:02:04.956][private$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[2024-09-21 16:02:04.957][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-09-21 16:02:04.967][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:04.969][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:04.970][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-21 16:02:04.971][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:04.972][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-21 16:02:04.983][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-21 16:02:04.985][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-21 16:02:04.985][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-21 16:02:04.986][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-21 16:02:04.987][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-21 16:02:04.988][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-21 16:02:04.989][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.992][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.995][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:04.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:04.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:04.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:04.999][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:05.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:05.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:05.004][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-21 16:02:05.005][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-21 16:02:05.005][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-09-21 16:02:05.018][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.019][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.021][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:05.022][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-09-21 16:02:05.034][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.038][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.041][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:05.046][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-09-21 16:02:05.048][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-09-21 16:02:05.048][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-09-21 16:02:05.049][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-09-21 16:02:05.050][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:05.052][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:05.053][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-21 16:02:05.054][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:05.055][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-21 16:02:05.056][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-21 16:02:05.057][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-21 16:02:05.058][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-21 16:02:05.058][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-21 16:02:05.059][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-21 16:02:05.060][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-21 16:02:05.062][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.065][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.072][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.075][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:05.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:05.079][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-21 16:02:05.079][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-09-21 16:02:05.080][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-09-21 16:02:05.095][biodb::testThat]
biodb.INFO [2024-09-21 16:02:05.096][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-09-21 16:02:05.097][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:05.097][biodb::testThat]
biodb.TRACE[2024-09-21 16:02:05.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:05.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:05.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:05.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:05.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:05.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:05.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:05.134][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-09-21 16:02:05.137][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-09-21 16:02:05.138][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-09-21 16:02:05.139][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:05.140][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:05.141][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-09-21 16:02:05.143][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-09-21 16:02:05.143][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-09-21 16:02:05.144][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-09-21 16:02:05.145][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-09-21 16:02:05.146][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-09-21 16:02:05.147][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-09-21 16:02:05.148][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-09-21 16:02:05.149][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-09-21 16:02:05.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:05.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:05.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:05.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:05.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:05.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:05.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:05.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:02:05.163][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-09-21 16:02:05.164][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-09-21 16:02:05.180][biodb::testThat]
biodb.INFO [2024-09-21 16:02:05.181][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-09-21 16:02:05.182][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:05.183][biodb::testThat]
biodb.TRACE[2024-09-21 16:02:05.200][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:02:05.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:02:05.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.203][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:02:05.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:02:05.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.207][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-21 16:02:05.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-21 16:02:05.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.214][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-21 16:02:05.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-21 16:02:05.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.249][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:02:05.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:02:05.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:02:05.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:02:05.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.260][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-21 16:02:05.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-21 16:02:05.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:05.263][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-21 16:02:05.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-21 16:02:05.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:05.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-21 16:02:05.272][biodb::testThat]
biodb.INFO [2024-09-21 16:02:05.273][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-09-21 16:02:05.274][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:05.276][biodb::testThat]
biodb.INFO [2024-09-21 16:02:05.287][biodb::testThat]
biodb.INFO [2024-09-21 16:02:05.288][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-09-21 16:02:05.289][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:05.289][biodb::testThat]
biodb.INFO [2024-09-21 16:02:05.297][biodb::testThat]
biodb.INFO [2024-09-21 16:02:05.298][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-09-21 16:02:05.298][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:05.299][biodb::testThat]
biodb.DEBUG[2024-09-21 16:02:05.302][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-09-21 16:02:29.511][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-09-21 16:02:29.749][biodb::testThat]
biodb.INFO [2024-09-21 16:02:29.750][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-09-21 16:02:29.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:02:29.751][biodb::testThat]
biodb.DEBUG[2024-09-21 16:02:38.479][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-09-21 16:02:38.780][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:38.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:38.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:38.782][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:38.783][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:38.784][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:38.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:38.785][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:38.786][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:38.787][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:38.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:38.788][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:38.790][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:02:38.790][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:02:38.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:38.792][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:38.792][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:02:38.793][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:02:38.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:38.794][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:02:38.795][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:38.796][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:02:38.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:02:38.797][ef$get] fields variable is a list.
biodb.INFO [2024-09-21 16:02:38.798][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-21 16:02:38.807][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-09-21 16:02:38.808][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-09-21 16:02:38.808][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-21 16:02:38.809][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:02:38.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:02:38.810][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:02:38.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:02:38.812][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:02:38.812][FUN] Functions in observer 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 
  3.982   0.308  37.828

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)