Back to Long Tests report for BioC 3.16

This page was generated on 2023-04-15 21:30:03 -0400 (Sat, 15 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for biodbNci on lconway


To the developers/maintainers of the biodbNci package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 12/28HostnameOS / ArchCHECK
biodbNci 1.2.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-04-15 06:55:01 -0400 (Sat, 15 Apr 2023)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_16
git_last_commit: 768ea26
git_last_commit_date: 2022-11-01 11:26:38 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.5.1 Monterey / x86_64  OK  

Summary

Package: biodbNci
Version: 1.2.0
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 biodbNci_1.2.0.tar.gz
StartedAt: 2023-04-15 08:01:34 -0400 (Sat, 15 Apr 2023)
EndedAt: 2023-04-15 08:27:32 -0400 (Sat, 15 Apr 2023)
EllapsedTime: 1557.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2023-04-15 08:02:33.562][biodb::testContext]
biodb.INFO [2023-04-15 08:02:33.579][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:33.580][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-04-15 08:02:33.581][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:02:33.581][biodb::testContext]
biodb.INFO [2023-04-15 08:02:33.587][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:33.589][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:33.595][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:33.596][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:02:33.597][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:02:33.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.600][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:02:33.613][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:02:33.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.616][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:02:33.617][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:02:33.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.620][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:02:33.621][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:02:33.621][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:02:33.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.624][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:02:33.625][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:02:33.626][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:02:33.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.629][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:02:33.630][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:02:33.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.633][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:02:33.633][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:02:33.634][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:02:33.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.637][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:02:33.637][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:02:33.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.640][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:02:33.641][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:02:33.642][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:02:33.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.644][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:33.645][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:02:33.646][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:02:33.647][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:02:33.647][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:02:33.648][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:02:33.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.651][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:02:33.651][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:02:33.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.654][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:02:33.655][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:02:33.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.658][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:02:33.658][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:02:33.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.661][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:02:33.662][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:02:33.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.664][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:02:33.665][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:02:33.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.668][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:02:33.668][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:02:33.682][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:02:33.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.685][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:02:33.686][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:02:33.687][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:02:33.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.692][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:02:33.719][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.729][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-15 08:02:33.730][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.731][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:33.731][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.732][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.733][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.734][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.734][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:33.735][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:33.736][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.736][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:02:33.737][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:33.738][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.738][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.739][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:33.739][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:33.739][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:33.739][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:33.739][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:33.740][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:33.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:33.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:33.742][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:33.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:33.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:33.744][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.745][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:33.746][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:33.746][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.747][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.748][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:02:33.749][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.750][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:33.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:33.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.753][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.753][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.755][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:33.756][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:33.756][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.757][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:02:33.758][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:33.758][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.759][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:02:33.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:02:33.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:02:33.760][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:02:33.760][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:02:33.761][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:33.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:33.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:33.763][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:33.763][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:33.764][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:33.765][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.765][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:33.767][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:33.767][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.768][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.769][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:02:33.770][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.771][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-15 08:02:33.772][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.772][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:33.773][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.774][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.774][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.776][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:02:33.777][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:33.777][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.778][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:02:33.779][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:33.779][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.781][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.782][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:33.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:33.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:33.784][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:33.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:33.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:33.786][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.786][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.787][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:33.788][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:33.788][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.789][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.790][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:02:33.791][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.792][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:02:33.792][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:33.794][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.794][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.795][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.796][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.797][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:02:33.797][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:33.798][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.799][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:02:33.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:33.800][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.801][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:33.802][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.802][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:02:33.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:33.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:33.804][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:33.805][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:33.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:33.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:33.807][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:33.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:33.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:33.810][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:33.812][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:33.813][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.814][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[2023-04-15 08:02:33.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.873][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:02:33.877][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:02:33.878][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:02:33.879][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:02:33.880][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:02:33.881][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:02:33.882][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:33.883][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:33.884][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:02:33.885][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:02:33.886][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:02:33.887][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:02:33.888][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:02:33.889][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:02:33.890][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:02:33.891][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:02:33.892][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:02:33.893][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:02:33.894][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:02:33.895][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:02:33.896][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:02:33.897][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:02:33.898][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:02:33.899][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:02:33.899][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:02:33.900][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:02:33.901][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:02:33.902][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:02:33.903][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:02:33.904][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:02:33.905][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:02:33.906][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:02:33.907][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:02:33.908][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:02:33.909][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:02:33.910][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:02:33.911][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:02:33.912][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:02:33.913][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:02:33.914][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:02:33.915][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:02:33.916][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:02:33.917][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:02:33.918][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:02:33.919][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:02:33.920][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:02:33.921][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:02:33.922][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:02:33.923][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:02:33.924][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:02:33.925][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:02:33.926][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:02:33.927][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:02:33.928][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:02:33.929][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:02:33.930][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:02:33.931][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:02:33.932][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:02:33.933][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:02:33.934][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:02:33.935][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:02:33.936][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:02:33.937][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:02:33.942][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:02:33.943][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:02:33.944][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:02:33.944][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:02:33.945][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:02:33.946][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:02:33.947][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:02:33.948][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:02:33.949][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:02:33.950][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:02:33.951][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:02:33.952][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:02:33.953][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:02:33.954][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:02:33.955][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:02:33.956][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:02:33.957][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:02:33.957][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:02:33.958][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:02:33.959][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:02:33.963][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:02:33.964][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:02:33.967][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:02:33.967][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.969][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:33.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:33.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:33.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:33.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:33.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:33.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:33.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:33.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:33.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:33.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:33.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:33.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:33.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:33.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:33.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:33.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:33.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:33.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.032][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[2023-04-15 08:02:34.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:02:34.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:02:34.046][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2023-04-15 08:02:34.077][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2023-04-15 08:02:34.078][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:34.079][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2023-04-15 08:02:34.080][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:34.080][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:02:34.081][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:34.082][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-04-15 08:02:34.082][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:34.083][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:02:34.084][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2023-04-15 08:02:34.084][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:02:34.085][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:34.086][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2023-04-15 08:02:34.087][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:02:34.087][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2023-04-15 08:02:34.087][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2023-04-15 08:02:34.087][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2023-04-15 08:02:34.087][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2023-04-15 08:02:34.087][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2023-04-15 08:02:34.087][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2023-04-15 08:02:34.087][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2023-04-15 08:02:34.088][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:02:34.089][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:34.089][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:02:34.090][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:34.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:34.091][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:02:34.092][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:02:34.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:02:34.093][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:02:34.094][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2023-04-15 08:02:34.094][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2023-04-15 08:02:34.094][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2023-04-15 08:02:34.094][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2023-04-15 08:02:34.095][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:02:34.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:02:34.096][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:02:34.097][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:02:34.101][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2023-04-15 08:02:34.119][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2023-04-15 08:02:34.120][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2023-04-15 08:02:34.123][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2023-04-15 08:02:34.126][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2023-04-15 08:02:34.129][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:34.129][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:02:34.130][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-04-15 08:02:34.131][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-04-15 08:02:34.132][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-04-15 08:02:34.133][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2023-04-15 08:02:34.139][biodb::testThat]
biodb.INFO [2023-04-15 08:02:34.139][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-04-15 08:02:34.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:34.141][biodb::testThat]
biodb.TRACE[2023-04-15 08:02:34.144][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2023-04-15 08:02:34.145][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:02:34.147][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2023-04-15 08:02:34.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:34.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.167][FUN] Functions in observer BiodbConfig: [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[2023-04-15 08:02:34.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.222][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.243][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.246][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.251][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:34.296][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2023-04-15 08:02:34.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:34.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:34.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.300][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:34.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:34.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.303][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:34.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:34.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.306][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:34.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:34.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.333][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.357][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.360][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.363][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.383][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.384][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.385][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.385][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.393][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.396][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.402][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.402][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.403][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.404][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.404][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.420][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.421][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.421][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.422][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.438][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.439][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.440][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.456][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.457][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.457][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.458][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.470][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.470][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.471][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.472][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.475][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.477][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.480][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.481][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.481][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.482][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.485][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.486][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.487][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.487][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.491][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.492][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.492][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.493][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.504][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2023-04-15 08:02:34.526][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2023-04-15 08:02:34.527][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2023-04-15 08:02:34.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:02:34.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:02:34.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:02:34.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:02:34.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:02:34.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:02:34.535][FUN] Functions in observer BiodbConfig: [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[2023-04-15 08:02:34.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.563][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.566][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.614][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.617][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.623][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:02:34.647][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2023-04-15 08:02:34.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:34.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:34.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.664][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:02:34.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:02:34.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.666][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:34.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:02:34.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:34.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:02:34.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.679][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.703][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.705][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.708][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:02:34.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.734][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.734][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.735][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.736][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.744][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.747][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.749][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.752][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.753][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.753][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.754][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.755][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.770][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.771][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.772][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.772][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.780][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.789][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.791][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.791][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.811][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.811][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.812][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.813][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.829][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.830][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.830][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.831][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.832][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.847][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.848][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.849][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.849][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.857][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:02:34.858][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:02:34.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.859][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.863][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.864][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:02:34.864][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.865][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.868][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:02:34.869][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:02:34.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.870][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.874][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:02:34.874][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:02:34.875][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.876][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.879][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.880][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:02:34.880][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.881][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.888][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.889][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:02:34.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.890][ef$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:02:34.893][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:02:34.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:02:34.894][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:02:34.895][ef$get] fields variable is a list.
biodb.INFO [2023-04-15 08:02:34.899][biodb::testThat]
biodb.INFO [2023-04-15 08:02:34.899][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-15 08:02:34.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:02:34.901][biodb::testThat]
biodb.DEBUG[2023-04-15 08:02:34.902][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2023-04-15 08:02:34.908][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2023-04-15 08:02:34.910][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2023-04-15 08:02:34.911][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2023-04-15 08:02:34.912][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2023-04-15 08:02:34.912][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2023-04-15 08:02:34.914][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2023-04-15 08:03:14.644][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactus132716b5c372cgz".
biodb.TRACE[2023-04-15 08:03:14.645][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2023-04-15 08:03:14.646][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2023-04-15 08:03:14.647][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2023-04-15 08:03:14.647][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2023-04-15 08:03:14.649][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker13271732a60c4marker".
biodb.TRACE[2023-04-15 08:03:14.650][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2023-04-15 08:03:14.650][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-04-15 08:03:14.651][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2023-04-15 08:03:14.652][self$download] Extract whole database of nci.cactus.
biodb.INFO [2023-04-15 08:03:14.653][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2023-04-15 08:03:14.654][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2023-04-15 08:04:13.381][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2023-04-15 08:04:13.383][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2023-04-15 08:25:47.313][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2023-04-15 08:25:47.616][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2023-04-15 08:27:26.997][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-04-15 08:27:26.998][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2023-04-15 08:27:27.000][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker1327163371eedmarker".
biodb.TRACE[2023-04-15 08:27:27.000][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2023-04-15 08:27:27.001][self$addFilesToCache] Done adding files.
biodb.TRACE[2023-04-15 08:27:27.002][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2023-04-15 08:27:27.003][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-04-15 08:27:27.171][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2023-04-15 08:27:27.172][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2023-04-15 08:27:27.173][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2023-04-15 08:27:27.174][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2023-04-15 08:27:27.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:27:27.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:27.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:27.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:27.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:27.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-15 08:27:27.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.193][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:27:27.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:27:27.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:27:27.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:27:27.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:27:27.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:27:27.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:27:27.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:27:27.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:27:27.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:27:27.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:27:27.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:27:27.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:27:27.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:27:27.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:27:27.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:27:27.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.216][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.219][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.225][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:27:27.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-15 08:27:27.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:27.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:27.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:27.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:27.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.245][FUN] Functions in observer BiodbConfig: [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[2023-04-15 08:27:27.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.258][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:27:27.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:27:27.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.260][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-04-15 08:27:27.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-04-15 08:27:27.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.264][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:27:27.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:27:27.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.267][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-15 08:27:27.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-15 08:27:27.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:27:27.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:27:27.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-15 08:27:27.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-15 08:27:27.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:27:27.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:27:27.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:27:27.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:27:27.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:27:27.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:27:27.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:27:27.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:27:27.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:27:27.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:27:27.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:27:27.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:27:27.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-15 08:27:27.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-15 08:27:27.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.317][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:27:27.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:27:27.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-04-15 08:27:27.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-04-15 08:27:27.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:27:27.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:27:27.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-04-15 08:27:27.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-04-15 08:27:27.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.329][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.333][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.339][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-04-15 08:27:27.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-15 08:27:27.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-15 08:27:27.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-15 08:27:27.384][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2023-04-15 08:27:27.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:27:27.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:27:27.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:27:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:27:27.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:27:27.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:27:27.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-15 08:27:27.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-15 08:27:27.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:27:27.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-15 08:27:27.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:27:27.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-15 08:27:27.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:27:27.450][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.465][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-15 08:27:27.466][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:27:27.467][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.469][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.470][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-04-15 08:27:27.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:27:27.471][biodb::testThat]
biodb.WARN [2023-04-15 08:27:27.553][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2023-04-15 08:27:27.566][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2023-04-15 08:27:27.571][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.589][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-04-15 08:27:27.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:27:27.590][biodb::testThat]
biodb.TRACE[2023-04-15 08:27:27.606][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:27:27.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:27:27.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.609][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:27:27.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:27:27.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.612][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:27:27.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:27:27.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.616][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:27:27.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:27:27.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.639][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:27:27.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:27:27.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-15 08:27:27.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-15 08:27:27.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.644][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-15 08:27:27.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-15 08:27:27.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-15 08:27:27.647][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-15 08:27:27.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-15 08:27:27.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-15 08:27:27.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-15 08:27:27.652][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.652][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-15 08:27:27.653][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:27:27.654][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.657][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.658][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-15 08:27:27.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:27:27.659][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.662][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.663][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-15 08:27:27.664][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:27:27.685][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.688][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.689][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-15 08:27:27.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-15 08:27:27.690][biodb::testThat]
biodb.INFO [2023-04-15 08:27:27.693][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:27:27.694][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2023-04-15 08:27:27.695][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2023-04-15 08:27:27.696][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:27:27.696][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:27.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:27.698][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:27.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:27.699][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-15 08:27:27.728][biodb::testContext]
biodb.INFO [2023-04-15 08:27:27.728][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:27:27.729][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-04-15 08:27:27.730][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-15 08:27:27.730][biodb::testContext]
biodb.INFO [2023-04-15 08:27:27.857][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:27:27.868][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-04-15 08:27:27.873][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:27:27.874][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-15 08:27:27.875][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-15 08:27:27.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.878][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-15 08:27:27.878][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-15 08:27:27.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.881][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-15 08:27:27.882][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-15 08:27:27.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.884][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-15 08:27:27.885][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-15 08:27:27.886][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-15 08:27:27.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.888][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-15 08:27:27.889][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-15 08:27:27.890][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-15 08:27:27.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.892][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-15 08:27:27.893][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-15 08:27:27.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.896][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-15 08:27:27.896][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-15 08:27:27.897][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-15 08:27:27.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.900][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-15 08:27:27.900][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-15 08:27:27.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.903][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-15 08:27:27.904][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-15 08:27:27.905][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-15 08:27:27.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.907][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:27:27.908][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-15 08:27:27.909][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-15 08:27:27.910][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-15 08:27:27.910][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-15 08:27:27.911][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-15 08:27:27.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.914][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-15 08:27:27.915][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-15 08:27:27.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.918][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-15 08:27:27.918][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-15 08:27:27.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.921][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-15 08:27:27.922][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-15 08:27:27.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.925][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-15 08:27:27.926][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-15 08:27:27.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.929][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-15 08:27:27.929][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-15 08:27:27.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:27.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:27.932][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-15 08:27:27.933][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-15 08:27:27.998][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-15 08:27:27.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:27.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.001][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-15 08:27:28.001][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-15 08:27:28.002][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-15 08:27:28.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.005][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-15 08:27:28.006][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.007][self$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[2023-04-15 08:27:28.007][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.008][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:27:28.009][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.009][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.010][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.011][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.011][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:27:28.012][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:27:28.013][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.013][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-15 08:27:28.014][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:27:28.015][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.016][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.017][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:27:28.017][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:27:28.017][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:27:28.017][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:27:28.017][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:27:28.018][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:27:28.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.020][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:27:28.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.022][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.023][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:27:28.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:27:28.025][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.026][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.027][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-15 08:27:28.028][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.029][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:27:28.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:27:28.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.033][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.034][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.035][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:27:28.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:27:28.036][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.037][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-15 08:27:28.038][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:27:28.038][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.039][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.040][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-15 08:27:28.040][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-15 08:27:28.040][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-15 08:27:28.040][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-15 08:27:28.040][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-15 08:27:28.041][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:27:28.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:27:28.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.044][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.045][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.046][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:27:28.046][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:27:28.047][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.048][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.048][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-15 08:27:28.050][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.050][self$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[2023-04-15 08:27:28.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:27:28.052][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.053][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.054][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.054][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.055][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-15 08:27:28.056][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:27:28.056][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.057][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-15 08:27:28.058][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:27:28.058][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.060][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.060][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:27:28.061][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.062][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:27:28.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.063][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.064][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.065][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.066][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:27:28.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:27:28.067][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.067][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.068][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-15 08:27:28.069][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.070][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-15 08:27:28.071][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.072][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:27:28.078][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.079][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.080][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.080][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.081][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-15 08:27:28.082][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:27:28.082][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.083][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-15 08:27:28.084][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:27:28.084][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.085][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.086][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.087][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-15 08:27:28.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.089][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:27:28.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.092][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.092][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:27:28.093][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:27:28.094][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.094][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.095][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:27:28.096][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.151][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-15 08:27:28.152][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-15 08:27:28.153][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-15 08:27:28.154][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-15 08:27:28.155][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-15 08:27:28.157][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-15 08:27:28.158][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-15 08:27:28.159][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-15 08:27:28.160][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-15 08:27:28.161][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-15 08:27:28.162][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-15 08:27:28.163][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-15 08:27:28.164][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-15 08:27:28.165][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-15 08:27:28.166][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-15 08:27:28.167][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-15 08:27:28.168][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-15 08:27:28.169][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-15 08:27:28.170][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-15 08:27:28.171][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-15 08:27:28.172][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-15 08:27:28.173][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-15 08:27:28.174][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-15 08:27:28.175][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-15 08:27:28.176][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-15 08:27:28.177][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-15 08:27:28.178][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-15 08:27:28.179][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-15 08:27:28.180][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-15 08:27:28.181][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-15 08:27:28.182][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-15 08:27:28.183][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-15 08:27:28.184][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-15 08:27:28.185][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-15 08:27:28.187][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-15 08:27:28.188][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-15 08:27:28.189][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-15 08:27:28.190][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-15 08:27:28.191][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-15 08:27:28.192][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-15 08:27:28.193][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-15 08:27:28.194][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-15 08:27:28.195][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-15 08:27:28.196][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-15 08:27:28.197][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-15 08:27:28.198][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-15 08:27:28.199][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-15 08:27:28.200][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-15 08:27:28.201][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-15 08:27:28.202][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-15 08:27:28.202][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-15 08:27:28.203][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-15 08:27:28.204][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-15 08:27:28.205][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-15 08:27:28.206][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-15 08:27:28.207][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-15 08:27:28.208][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-15 08:27:28.209][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-15 08:27:28.210][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-15 08:27:28.211][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-15 08:27:28.212][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-15 08:27:28.213][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-15 08:27:28.215][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-15 08:27:28.216][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-15 08:27:28.217][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-15 08:27:28.218][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-15 08:27:28.219][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-15 08:27:28.220][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-15 08:27:28.221][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-15 08:27:28.222][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-15 08:27:28.223][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-15 08:27:28.224][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-15 08:27:28.225][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-15 08:27:28.226][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-15 08:27:28.227][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-15 08:27:28.228][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-15 08:27:28.229][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-15 08:27:28.230][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-15 08:27:28.231][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-15 08:27:28.232][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-15 08:27:28.233][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-15 08:27:28.234][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-15 08:27:28.235][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-15 08:27:28.236][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-15 08:27:28.237][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-15 08:27:28.238][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-15 08:27:28.238][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.240][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-15 08:27:28.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-15 08:27:28.329][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2023-04-15 08:27:28.337][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2023-04-15 08:27:28.339][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.340][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2023-04-15 08:27:28.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.341][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-15 08:27:28.342][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.343][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-04-15 08:27:28.344][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.344][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.345][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2023-04-15 08:27:28.346][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-15 08:27:28.347][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.348][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2023-04-15 08:27:28.348][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-15 08:27:28.349][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2023-04-15 08:27:28.349][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2023-04-15 08:27:28.349][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2023-04-15 08:27:28.349][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2023-04-15 08:27:28.349][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2023-04-15 08:27:28.349][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2023-04-15 08:27:28.349][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2023-04-15 08:27:28.350][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-15 08:27:28.351][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.352][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-04-15 08:27:28.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.354][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-15 08:27:28.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-15 08:27:28.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-15 08:27:28.356][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-15 08:27:28.356][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2023-04-15 08:27:28.356][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2023-04-15 08:27:28.356][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2023-04-15 08:27:28.356][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2023-04-15 08:27:28.357][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-15 08:27:28.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-15 08:27:28.359][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-15 08:27:28.359][self$setPropertyValue]
biodb.DEBUG[2023-04-15 08:27:28.360][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2023-04-15 08:27:28.362][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2023-04-15 08:27:28.363][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2023-04-15 08:27:28.364][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2023-04-15 08:27:28.365][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2023-04-15 08:27:28.366][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:27:28.367][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-04-15 08:27:28.367][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-04-15 08:27:28.368][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-04-15 08:27:28.369][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-04-15 08:27:28.370][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2023-04-15 08:27:28.371][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-15 08:27:28.372][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2023-04-15 08:27:28.372][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2023-04-15 08:27:28.373][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-15 08:27:28.374][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-15 08:27:28.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-15 08:27:28.375][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-15 08:27:28.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-15 08:27:28.376][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-15 08:27:28.377][FUN] Functions in observer 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 92 ]
> 
> proc.time()
    user   system  elapsed 
1114.275  189.389 1496.410

'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 biodbNci_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.2.0’
* 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 ‘biodbNci’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c extractEntries.cpp -o extractEntries.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-100-example.cpp -o test-100-example.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-runner.cpp -o test-runner.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 (biodbNci)