Back to Long Tests report for BioC 3.21

This page was generated on 2025-04-19 23:55 -0400 (Sat, 19 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 9/30HostnameOS / ArchCHECK
biodbNci 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-19 09:55 -0400 (Sat, 19 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_21
git_last_commit: a398ae4
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on lconway

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

raw results


Summary

Package: biodbNci
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2025-04-19 16:01:32 -0400 (Sat, 19 Apr 2025)
EndedAt: 2025-04-19 16:27:24 -0400 (Sat, 19 Apr 2025)
EllapsedTime: 1552.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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 [2025-04-19 16:02:24.517][biodb::testContext]
biodb.INFO [2025-04-19 16:02:24.520][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-19 16:02:24.521][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-19 16:02:24.522][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-19 16:02:24.522][biodb::testContext]
biodb.INFO [2025-04-19 16:02:24.527][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-19 16:02:24.528][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-19 16:02:24.533][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:02:24.534][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-19 16:02:24.535][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-19 16:02:24.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.538][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-19 16:02:24.550][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-19 16:02:24.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.553][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-19 16:02:24.554][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-19 16:02:24.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.557][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-19 16:02:24.557][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-19 16:02:24.558][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-19 16:02:24.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.561][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-19 16:02:24.562][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-19 16:02:24.563][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-19 16:02:24.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.566][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-19 16:02:24.566][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-19 16:02:24.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.569][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-19 16:02:24.570][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-19 16:02:24.571][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-19 16:02:24.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.573][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-19 16:02:24.574][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-19 16:02:24.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.577][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-19 16:02:24.577][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-19 16:02:24.578][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-19 16:02:24.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.581][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-19 16:02:24.581][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-19 16:02:24.582][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-19 16:02:24.583][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-19 16:02:24.584][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-19 16:02:24.584][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-19 16:02:24.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.587][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-19 16:02:24.588][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-19 16:02:24.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.590][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-19 16:02:24.591][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-19 16:02:24.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.594][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-19 16:02:24.594][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-19 16:02:24.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.597][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-19 16:02:24.598][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-19 16:02:24.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.600][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-19 16:02:24.601][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-19 16:02:24.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.604][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-19 16:02:24.604][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-19 16:02:24.621][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-19 16:02:24.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.624][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-19 16:02:24.625][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-19 16:02:24.626][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-19 16:02:24.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.631][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-19 16:02:24.654][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.671][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-19 16:02:24.672][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.673][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:02:24.674][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.675][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.675][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.676][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.677][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-19 16:02:24.677][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:02:24.678][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.679][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-19 16:02:24.680][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:02:24.681][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.681][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.682][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-19 16:02:24.682][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-19 16:02:24.682][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-19 16:02:24.682][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-19 16:02:24.682][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-19 16:02:24.683][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:02:24.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:24.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:24.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:02:24.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:24.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:24.687][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.688][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.688][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:02:24.689][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:02:24.690][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.690][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.691][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-19 16:02:24.692][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.693][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-19 16:02:24.694][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.695][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:02:24.695][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.696][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.697][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.697][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.698][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-19 16:02:24.699][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:02:24.700][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.700][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-19 16:02:24.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:02:24.702][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.702][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.703][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-19 16:02:24.703][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-19 16:02:24.703][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-19 16:02:24.703][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-19 16:02:24.703][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-19 16:02:24.704][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:02:24.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:24.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:24.706][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:02:24.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:24.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:24.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.709][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.709][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:02:24.710][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:02:24.711][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.711][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.712][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-19 16:02:24.714][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.714][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-19 16:02:24.715][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.716][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:02:24.717][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.717][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.718][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.719][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.719][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-19 16:02:24.720][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:02:24.721][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.721][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-19 16:02:24.722][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:02:24.723][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.724][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.724][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.725][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:02:24.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:24.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:24.727][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:02:24.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:24.728][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:24.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.730][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:02:24.731][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:02:24.732][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.733][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.734][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-19 16:02:24.735][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.736][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-19 16:02:24.736][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.737][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:02:24.738][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.739][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.739][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.740][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.741][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-19 16:02:24.742][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:02:24.743][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.743][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-19 16:02:24.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:02:24.745][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.745][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:24.746][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.747][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:02:24.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:24.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:24.749][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:02:24.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:24.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:24.751][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:02:24.752][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.753][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:02:24.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:02:24.754][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:24.755][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:24.758][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:02:24.758][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.820][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-19 16:02:24.824][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-19 16:02:24.825][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-19 16:02:24.826][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-19 16:02:24.827][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-19 16:02:24.828][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-19 16:02:24.829][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-19 16:02:24.830][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-19 16:02:24.831][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-19 16:02:24.832][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-19 16:02:24.833][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-19 16:02:24.834][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-19 16:02:24.835][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-19 16:02:24.836][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-19 16:02:24.838][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-19 16:02:24.839][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-19 16:02:24.840][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-19 16:02:24.840][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-19 16:02:24.841][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-19 16:02:24.842][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-19 16:02:24.843][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-19 16:02:24.844][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-19 16:02:24.845][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-19 16:02:24.846][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-19 16:02:24.847][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-19 16:02:24.848][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-19 16:02:24.849][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-19 16:02:24.850][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-19 16:02:24.851][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-19 16:02:24.852][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-19 16:02:24.853][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-19 16:02:24.854][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-19 16:02:24.855][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-19 16:02:24.856][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-19 16:02:24.857][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-19 16:02:24.858][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-19 16:02:24.859][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-19 16:02:24.860][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-19 16:02:24.861][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-19 16:02:24.862][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-19 16:02:24.863][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-19 16:02:24.864][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-19 16:02:24.865][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-19 16:02:24.866][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-19 16:02:24.867][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-19 16:02:24.868][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-19 16:02:24.869][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-19 16:02:24.870][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-19 16:02:24.871][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-19 16:02:24.872][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-19 16:02:24.873][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-19 16:02:24.875][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-19 16:02:24.876][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-19 16:02:24.877][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-19 16:02:24.878][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-19 16:02:24.879][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-19 16:02:24.880][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-19 16:02:24.881][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-19 16:02:24.882][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-19 16:02:24.883][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-19 16:02:24.884][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-19 16:02:24.885][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-19 16:02:24.886][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-19 16:02:24.888][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-19 16:02:24.889][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-19 16:02:24.890][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-19 16:02:24.891][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-19 16:02:24.892][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-19 16:02:24.893][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-19 16:02:24.894][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-19 16:02:24.895][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-19 16:02:24.896][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-19 16:02:24.897][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-19 16:02:24.898][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-19 16:02:24.899][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-19 16:02:24.900][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-19 16:02:24.901][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-19 16:02:24.902][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-19 16:02:24.903][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-19 16:02:24.904][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-19 16:02:24.905][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-19 16:02:24.906][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-19 16:02:24.907][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-19 16:02:24.912][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-19 16:02:24.913][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-19 16:02:24.915][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:02:24.916][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.918][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.989][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[2025-04-19 16:02:24.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:24.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:24.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:24.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:24.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:24.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:24.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:24.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:02:25.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:02:25.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:25.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:25.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:25.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:25.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:25.004][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[2025-04-19 16:02:25.006][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-19 16:02:25.013][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-19 16:02:25.015][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:25.015][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-19 16:02:25.016][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:25.017][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:02:25.017][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:25.018][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-19 16:02:25.019][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:25.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:02:25.021][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-19 16:02:25.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:02:25.022][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:25.023][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-19 16:02:25.023][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:02:25.024][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-19 16:02:25.024][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-19 16:02:25.024][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-19 16:02:25.024][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-19 16:02:25.024][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-19 16:02:25.024][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-19 16:02:25.024][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-19 16:02:25.025][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-19 16:02:25.026][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:25.026][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-19 16:02:25.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:25.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:25.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:02:25.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:02:25.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:02:25.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:02:25.032][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-19 16:02:25.032][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-19 16:02:25.032][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-19 16:02:25.032][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-19 16:02:25.032][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:02:25.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:02:25.034][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-19 16:02:25.034][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:02:25.039][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-19 16:02:25.057][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-19 16:02:25.058][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-19 16:02:25.062][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-19 16:02:25.065][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-19 16:02:25.067][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-19 16:02:25.068][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-19 16:02:25.069][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-19 16:02:25.070][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-19 16:02:25.071][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-19 16:02:25.072][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-19 16:02:25.105][biodb::testThat]
biodb.INFO [2025-04-19 16:02:25.106][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-19 16:02:25.107][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:02:25.108][biodb::testThat]
biodb.TRACE[2025-04-19 16:02:25.110][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-04-19 16:02:25.111][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-19 16:02:25.114][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-19 16:02:25.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-19 16:02:25.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:25.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:25.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:25.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:25.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:25.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-19 16:02:25.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.194][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.198][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.200][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.204][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.206][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.213][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-19 16:02:25.265][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-04-19 16:02:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:02:25.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:02:25.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.270][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:02:25.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:02:25.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.273][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-19 16:02:25.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-19 16:02:25.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.276][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-19 16:02:25.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-19 16:02:25.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.303][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.330][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.333][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.336][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.358][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.359][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.361][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.371][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.374][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.377][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.381][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.382][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.383][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.384][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.403][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.403][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.405][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.425][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.426][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.427][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.447][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.448][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.459][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.460][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.466][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.470][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.471][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.472][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.476][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.477][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.478][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.483][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.485][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.489][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.490][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.492][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.504][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-04-19 16:02:25.530][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-19 16:02:25.531][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-19 16:02:25.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-19 16:02:25.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:02:25.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:02:25.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:02:25.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:02:25.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:02:25.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-19 16:02:25.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.570][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.574][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.577][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.580][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.624][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.627][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.633][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-19 16:02:25.654][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-04-19 16:02:25.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:02:25.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:02:25.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.672][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:02:25.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:02:25.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-19 16:02:25.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-19 16:02:25.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-19 16:02:25.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-19 16:02:25.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.692][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.719][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.722][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.725][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:02:25.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.751][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.753][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.764][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.767][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.770][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.773][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.774][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.776][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.777][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.801][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.801][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.803][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.813][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.817][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.820][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.823][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.824][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.825][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.845][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.846][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.847][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.867][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.868][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.869][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.889][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.890][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.892][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.902][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:02:25.903][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:02:25.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.905][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.909][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.910][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:02:25.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.912][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.920][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:02:25.921][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:02:25.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.922][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.927][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:02:25.928][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:02:25.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.929][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.933][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:02:25.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.936][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.940][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.940][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:02:25.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.942][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:02:25.946][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:02:25.947][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:02:25.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:02:25.948][ef$get] fields variable is a list.
biodb.INFO [2025-04-19 16:02:25.955][biodb::testThat]
biodb.INFO [2025-04-19 16:02:25.956][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-19 16:02:25.957][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:02:25.958][biodb::testThat]
biodb.DEBUG[2025-04-19 16:02:25.959][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-04-19 16:02:25.964][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2025-04-19 16:02:25.968][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2025-04-19 16:02:25.968][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-04-19 16:02:25.969][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-04-19 16:02:25.970][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-04-19 16:02:25.971][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[2025-04-19 16:02:55.081][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactus135715891e5cgz".
biodb.TRACE[2025-04-19 16:02:55.083][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-19 16:02:55.084][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-19 16:02:55.085][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-19 16:02:55.085][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-04-19 16:02:55.087][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker135716d282cdamarker".
biodb.TRACE[2025-04-19 16:02:55.088][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-04-19 16:02:55.089][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-19 16:02:55.090][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-04-19 16:02:55.091][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-04-19 16:02:55.092][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-04-19 16:02:55.093][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-19 16:03:53.965][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-04-19 16:03:53.967][private$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[2025-04-19 16:25:23.969][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2025-04-19 16:25:24.312][private$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[2025-04-19 16:27:20.361][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-19 16:27:20.389][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-04-19 16:27:20.419][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker135716898d432marker".
biodb.TRACE[2025-04-19 16:27:20.421][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-04-19 16:27:20.422][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-04-19 16:27:20.424][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-04-19 16:27:20.426][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-04-19 16:27:20.459][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-04-19 16:27:20.461][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-19 16:27:20.463][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-04-19 16:27:20.465][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-04-19 16:27:20.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-19 16:27:20.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:20.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:20.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:20.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:20.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:20.644][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.TRACE[2025-04-19 16:27:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.666][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:27:20.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:27:20.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.670][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:27:20.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:27:20.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:27:20.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:27:20.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:27:20.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:27:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.684][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:27:20.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:27:20.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:27:20.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:27:20.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:27:20.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:27:20.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:27:20.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:27:20.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.699][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.702][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.709][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-19 16:27:20.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-19 16:27:20.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:20.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:20.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:20.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:20.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:20.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-19 16:27:20.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.752][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:27:20.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:27:20.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.756][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:27:20.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:27:20.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:27:20.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:27:20.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.763][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:27:20.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:27:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:27:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:27:20.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-19 16:27:20.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-19 16:27:20.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:27:20.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:27:20.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:27:20.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:27:20.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.780][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:27:20.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:27:20.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:27:20.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:27:20.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:27:20.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:27:20.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:27:20.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:27:20.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:27:20.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:27:20.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:27:20.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:27:20.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:27:20.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:27:20.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:27:20.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:27:20.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:27:20.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:27:20.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.812][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.815][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.822][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-19 16:27:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:27:20.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:27:20.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-19 16:27:20.854][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-04-19 16:27:20.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-19 16:27:20.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-19 16:27:20.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-19 16:27:20.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-19 16:27:20.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-19 16:27:20.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-19 16:27:20.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-19 16:27:20.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-19 16:27:20.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-19 16:27:20.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-19 16:27:20.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:20.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-19 16:27:20.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-19 16:27:20.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:20.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-19 16:27:20.890][biodb::testThat]
biodb.INFO [2025-04-19 16:27:20.891][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-19 16:27:20.892][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:27:20.893][biodb::testThat]
biodb.INFO [2025-04-19 16:27:20.899][biodb::testThat]
biodb.INFO [2025-04-19 16:27:20.899][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-19 16:27:20.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:27:20.901][biodb::testThat]
biodb.WARN [2025-04-19 16:27:20.921][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-04-19 16:27:20.937][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-04-19 16:27:20.945][biodb::testThat]
biodb.INFO [2025-04-19 16:27:20.946][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-19 16:27:20.947][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:27:20.948][biodb::testThat]
biodb.TRACE[2025-04-19 16:27:21.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:27:21.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:27:21.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:21.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:21.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:27:21.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:27:21.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:21.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:21.121][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-19 16:27:21.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-19 16:27:21.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:21.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:21.124][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-19 16:27:21.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-19 16:27:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:21.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:21.198][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:27:21.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:27:21.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:21.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:21.201][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:27:21.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:27:21.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:21.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:21.205][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-19 16:27:21.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-19 16:27:21.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:21.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:27:21.208][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-19 16:27:21.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-19 16:27:21.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:27:21.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-19 16:27:21.259][biodb::testThat]
biodb.INFO [2025-04-19 16:27:21.260][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-19 16:27:21.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:27:21.262][biodb::testThat]
biodb.INFO [2025-04-19 16:27:21.270][biodb::testThat]
biodb.INFO [2025-04-19 16:27:21.271][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-19 16:27:21.272][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:27:21.273][biodb::testThat]
biodb.INFO [2025-04-19 16:27:21.279][biodb::testThat]
biodb.INFO [2025-04-19 16:27:21.280][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-19 16:27:21.281][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:27:21.282][biodb::testThat]
biodb.INFO [2025-04-19 16:27:21.288][biodb::testThat]
biodb.INFO [2025-04-19 16:27:21.289][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-19 16:27:21.290][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:27:21.291][biodb::testThat]
biodb.INFO [2025-04-19 16:27:21.297][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-19 16:27:21.298][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-19 16:27:21.299][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-19 16:27:21.300][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-19 16:27:21.301][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:21.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:21.302][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:21.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:21.304][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-19 16:27:21.316][biodb::testContext]
biodb.INFO [2025-04-19 16:27:21.318][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-19 16:27:21.319][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-04-19 16:27:21.319][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-19 16:27:21.320][biodb::testContext]
biodb.INFO [2025-04-19 16:27:21.325][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-19 16:27:21.327][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-19 16:27:21.332][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:27:21.332][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-19 16:27:21.333][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-19 16:27:21.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.336][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-19 16:27:21.337][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-19 16:27:21.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.340][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-19 16:27:21.341][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-19 16:27:21.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.344][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-19 16:27:21.345][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-19 16:27:21.345][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-19 16:27:21.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.348][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-19 16:27:21.349][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-19 16:27:21.350][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-19 16:27:21.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.353][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-19 16:27:21.354][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-19 16:27:21.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.357][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-19 16:27:21.358][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-19 16:27:21.358][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-19 16:27:21.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.362][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-19 16:27:21.363][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-19 16:27:21.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.367][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-19 16:27:21.368][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-19 16:27:21.369][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-19 16:27:21.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.372][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-19 16:27:21.372][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-19 16:27:21.373][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-19 16:27:21.374][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-19 16:27:21.375][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-19 16:27:21.376][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-19 16:27:21.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.379][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-19 16:27:21.380][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-19 16:27:21.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.382][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-19 16:27:21.383][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-19 16:27:21.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.386][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-19 16:27:21.387][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-19 16:27:21.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.390][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-19 16:27:21.391][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-19 16:27:21.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.394][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-19 16:27:21.395][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-19 16:27:21.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:21.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:21.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:21.398][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-19 16:27:21.398][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-19 16:27:23.022][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-19 16:27:23.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.025][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-19 16:27:23.026][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-19 16:27:23.027][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-19 16:27:23.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.030][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-19 16:27:23.032][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.033][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-19 16:27:23.034][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.034][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:27:23.035][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.036][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.037][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.038][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.038][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-19 16:27:23.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:27:23.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.041][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-19 16:27:23.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:27:23.042][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.043][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.044][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-19 16:27:23.044][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-19 16:27:23.044][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-19 16:27:23.044][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-19 16:27:23.044][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-19 16:27:23.045][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:27:23.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.047][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:27:23.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.049][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.050][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.051][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:27:23.052][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:27:23.052][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.053][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.054][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-19 16:27:23.056][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.056][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-19 16:27:23.057][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.058][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:27:23.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.060][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.060][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.061][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.062][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-19 16:27:23.063][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:27:23.064][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.065][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-19 16:27:23.065][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:27:23.066][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.067][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.068][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-19 16:27:23.068][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-19 16:27:23.068][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-19 16:27:23.068][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-19 16:27:23.068][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-19 16:27:23.069][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:27:23.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.071][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:27:23.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.073][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.074][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.075][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:27:23.075][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:27:23.076][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.077][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.078][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-19 16:27:23.079][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.080][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-19 16:27:23.081][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.082][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:27:23.083][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.084][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.084][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.085][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.086][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-19 16:27:23.087][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:27:23.088][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.088][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-19 16:27:23.089][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:27:23.090][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.091][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.092][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.092][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:27:23.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.095][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:27:23.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.097][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.098][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.098][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:27:23.099][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:27:23.100][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.101][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.102][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-19 16:27:23.103][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.104][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-19 16:27:23.105][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.106][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:27:23.106][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.107][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.108][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.109][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.110][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-19 16:27:23.110][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:27:23.111][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.112][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-19 16:27:23.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:27:23.114][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.114][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.115][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.116][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:27:23.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.118][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:27:23.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.120][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.121][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.122][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:27:23.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:27:23.124][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.124][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.126][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:27:23.126][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.131][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[2025-04-19 16:27:23.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.138][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[2025-04-19 16:27:23.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.188][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-19 16:27:23.190][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-19 16:27:23.191][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-19 16:27:23.192][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-19 16:27:23.193][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-19 16:27:23.194][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-19 16:27:23.195][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-19 16:27:23.197][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-19 16:27:23.198][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-19 16:27:23.199][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-19 16:27:23.200][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-19 16:27:23.201][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-19 16:27:23.202][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-19 16:27:23.203][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-19 16:27:23.204][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-19 16:27:23.205][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-19 16:27:23.207][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-19 16:27:23.208][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-19 16:27:23.209][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-19 16:27:23.210][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-19 16:27:23.211][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-19 16:27:23.212][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-19 16:27:23.213][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-19 16:27:23.214][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-19 16:27:23.216][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-19 16:27:23.217][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-19 16:27:23.218][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-19 16:27:23.219][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-19 16:27:23.220][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-19 16:27:23.221][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-19 16:27:23.222][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-19 16:27:23.223][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-19 16:27:23.224][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-19 16:27:23.226][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-19 16:27:23.227][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-19 16:27:23.228][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-19 16:27:23.229][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-19 16:27:23.230][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-19 16:27:23.231][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-19 16:27:23.232][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-19 16:27:23.233][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-19 16:27:23.235][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-19 16:27:23.236][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-19 16:27:23.237][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-19 16:27:23.238][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-19 16:27:23.239][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-19 16:27:23.240][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-19 16:27:23.241][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-19 16:27:23.242][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-19 16:27:23.244][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-19 16:27:23.245][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-19 16:27:23.246][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-19 16:27:23.247][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-19 16:27:23.248][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-19 16:27:23.249][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-19 16:27:23.250][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-19 16:27:23.251][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-19 16:27:23.252][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-19 16:27:23.254][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-19 16:27:23.255][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-19 16:27:23.256][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-19 16:27:23.257][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-19 16:27:23.258][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-19 16:27:23.259][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-19 16:27:23.260][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-19 16:27:23.261][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-19 16:27:23.263][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-19 16:27:23.264][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-19 16:27:23.265][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-19 16:27:23.266][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-19 16:27:23.267][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-19 16:27:23.268][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-19 16:27:23.269][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-19 16:27:23.270][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-19 16:27:23.271][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-19 16:27:23.273][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-19 16:27:23.274][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-19 16:27:23.275][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-19 16:27:23.276][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-19 16:27:23.277][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-19 16:27:23.278][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-19 16:27:23.279][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-19 16:27:23.280][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-19 16:27:23.282][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-19 16:27:23.283][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-19 16:27:23.284][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:27:23.285][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.286][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.312][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[2025-04-19 16:27:23.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.317][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[2025-04-19 16:27:23.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:27:23.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:27:23.377][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-19 16:27:23.378][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-19 16:27:23.380][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.381][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-19 16:27:23.382][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.382][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:27:23.383][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.384][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-19 16:27:23.385][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.386][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.386][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-19 16:27:23.387][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:27:23.388][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.389][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-19 16:27:23.390][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:27:23.390][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-19 16:27:23.390][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-19 16:27:23.390][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-19 16:27:23.390][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-19 16:27:23.390][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-19 16:27:23.390][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-19 16:27:23.390][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-19 16:27:23.391][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-19 16:27:23.392][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.393][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-19 16:27:23.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.395][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:27:23.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:27:23.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:27:23.397][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:27:23.398][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-19 16:27:23.398][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-19 16:27:23.398][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-19 16:27:23.398][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-19 16:27:23.399][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:27:23.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:27:23.400][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-19 16:27:23.401][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:27:23.402][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-19 16:27:23.406][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-19 16:27:23.406][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-19 16:27:23.408][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-19 16:27:23.409][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-19 16:27:23.410][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-19 16:27:23.411][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-19 16:27:23.412][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-19 16:27:23.413][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-19 16:27:23.414][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-19 16:27:23.415][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-19 16:27:23.416][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-19 16:27:23.416][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-19 16:27:23.417][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-19 16:27:23.418][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-19 16:27:23.419][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:27:23.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:27:23.420][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:27:23.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:27:23.422][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:27:23.422][FUN] Functions in observer 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 
1074.746  244.894 1500.408

'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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.12.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-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)