Back to Long Tests report for BioC 3.19

This page was generated on 2024-03-02 23:55:03 -0500 (Sat, 02 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
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 12/31HostnameOS / ArchCHECK
biodbNci 1.7.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-03-02 09:55:01 -0500 (Sat, 02 Mar 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 7814b3a
git_last_commit_date: 2023-10-24 11:40:20 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1


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: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2024-03-02 16:06:19 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 16:07:37 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 78.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-03-02 16:07:33.523][biodb::testContext]
biodb.INFO [2024-03-02 16:07:33.527][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 16:07:33.528][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-03-02 16:07:33.529][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 16:07:33.530][biodb::testContext]
biodb.INFO [2024-03-02 16:07:33.537][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 16:07:33.539][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 16:07:33.546][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 16:07:33.547][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 16:07:33.549][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 16:07:33.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.553][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 16:07:33.576][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 16:07:33.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.580][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 16:07:33.582][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 16:07:33.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.586][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 16:07:33.587][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 16:07:33.588][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 16:07:33.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.593][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 16:07:33.594][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 16:07:33.595][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 16:07:33.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.600][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 16:07:33.601][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 16:07:33.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.605][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 16:07:33.606][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 16:07:33.607][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 16:07:33.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.612][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 16:07:33.613][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 16:07:33.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.617][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 16:07:33.619][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 16:07:33.620][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 16:07:33.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.624][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 16:07:33.626][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 16:07:33.627][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 16:07:33.628][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 16:07:33.629][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 16:07:33.630][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 16:07:33.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.635][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 16:07:33.636][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 16:07:33.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.641][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 16:07:33.642][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 16:07:33.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.646][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 16:07:33.647][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 16:07:33.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.652][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 16:07:33.653][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 16:07:33.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.657][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 16:07:33.658][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 16:07:33.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.663][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 16:07:33.664][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 16:07:33.674][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 16:07:33.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.679][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 16:07:33.680][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 16:07:33.681][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 16:07:33.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.689][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 16:07:33.732][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.757][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 16:07:33.758][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.760][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:33.761][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.762][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.763][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.764][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.765][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 16:07:33.767][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:33.768][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.769][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 16:07:33.770][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:33.771][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.773][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.774][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 16:07:33.774][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 16:07:33.774][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 16:07:33.774][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 16:07:33.774][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 16:07:33.775][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 16:07:33.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:33.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:33.779][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:33.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:33.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:33.782][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.783][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.784][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:33.785][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:33.786][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.788][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.789][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 16:07:33.791][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.792][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 16:07:33.793][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.795][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:33.796][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.798][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.801][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 16:07:33.802][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:33.803][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.804][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 16:07:33.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:33.807][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.809][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 16:07:33.809][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 16:07:33.809][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 16:07:33.809][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 16:07:33.809][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 16:07:33.810][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 16:07:33.811][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:33.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:33.814][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:33.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:33.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:33.817][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.818][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.820][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:33.821][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:33.822][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.823][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.824][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 16:07:33.826][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.828][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 16:07:33.829][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.830][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:33.831][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.833][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.834][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.835][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.836][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 16:07:33.837][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:33.839][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.840][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 16:07:33.841][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:33.842][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.843][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.845][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.846][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 16:07:33.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:33.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:33.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:33.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:33.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:33.853][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.854][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.855][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:33.856][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:33.857][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.858][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.860][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 16:07:33.862][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.863][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 16:07:33.864][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.866][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:33.867][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.868][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.870][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.872][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 16:07:33.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:33.874][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.875][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 16:07:33.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:33.878][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.879][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:33.880][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.881][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 16:07:33.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:33.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:33.885][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:33.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:33.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:33.888][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:33.889][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.890][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:33.892][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:33.893][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:33.894][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:33.898][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 16:07:33.899][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.944][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[2024-03-02 16:07:33.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:33.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:33.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:33.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:33.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:33.997][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 16:07:34.002][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 16:07:34.004][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 16:07:34.006][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 16:07:34.008][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 16:07:34.009][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 16:07:34.011][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 16:07:34.012][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 16:07:34.014][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 16:07:34.016][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 16:07:34.017][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 16:07:34.019][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 16:07:34.021][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 16:07:34.022][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 16:07:34.024][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 16:07:34.025][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 16:07:34.027][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 16:07:34.029][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 16:07:34.030][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 16:07:34.032][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 16:07:34.034][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 16:07:34.035][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 16:07:34.037][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 16:07:34.038][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 16:07:34.040][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 16:07:34.042][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 16:07:34.043][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 16:07:34.045][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 16:07:34.047][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 16:07:34.048][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 16:07:34.050][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 16:07:34.052][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 16:07:34.053][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 16:07:34.055][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 16:07:34.056][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 16:07:34.058][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 16:07:34.060][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 16:07:34.061][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 16:07:34.063][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 16:07:34.065][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 16:07:34.066][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 16:07:34.068][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 16:07:34.069][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 16:07:34.071][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 16:07:34.073][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 16:07:34.074][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 16:07:34.076][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 16:07:34.078][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 16:07:34.079][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 16:07:34.081][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 16:07:34.083][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 16:07:34.084][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 16:07:34.086][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 16:07:34.087][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 16:07:34.089][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 16:07:34.091][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 16:07:34.092][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 16:07:34.094][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 16:07:34.096][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 16:07:34.097][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 16:07:34.099][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 16:07:34.100][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 16:07:34.102][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 16:07:34.104][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 16:07:34.105][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 16:07:34.107][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 16:07:34.109][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 16:07:34.110][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 16:07:34.112][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 16:07:34.114][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 16:07:34.115][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 16:07:34.117][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 16:07:34.118][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 16:07:34.120][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 16:07:34.122][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 16:07:34.123][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 16:07:34.125][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 16:07:34.127][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 16:07:34.128][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 16:07:34.130][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 16:07:34.131][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 16:07:34.133][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 16:07:34.135][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 16:07:34.142][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 16:07:34.144][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 16:07:34.147][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 16:07:34.148][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.150][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.184][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[2024-03-02 16:07:34.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:34.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:34.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.287][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[2024-03-02 16:07:34.289][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-03-02 16:07:34.301][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-03-02 16:07:34.303][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:34.305][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-03-02 16:07:34.306][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:34.307][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:34.308][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:34.309][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-03-02 16:07:34.310][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:34.312][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:34.313][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-03-02 16:07:34.314][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:34.315][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:34.316][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-03-02 16:07:34.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:34.319][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-03-02 16:07:34.319][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-03-02 16:07:34.319][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-03-02 16:07:34.319][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-03-02 16:07:34.319][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-03-02 16:07:34.319][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-03-02 16:07:34.319][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-03-02 16:07:34.320][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:34.321][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:34.322][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 16:07:34.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:34.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:34.326][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:34.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:34.328][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:34.329][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:34.330][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-03-02 16:07:34.330][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-03-02 16:07:34.330][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-03-02 16:07:34.330][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-03-02 16:07:34.332][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:34.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:34.334][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:34.335][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:34.342][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-03-02 16:07:34.366][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-03-02 16:07:34.368][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-03-02 16:07:34.372][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-03-02 16:07:34.377][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-03-02 16:07:34.381][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 16:07:34.382][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 16:07:34.384][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 16:07:34.385][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 16:07:34.387][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 16:07:34.416][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-03-02 16:07:34.426][biodb::testThat]
biodb.INFO [2024-03-02 16:07:34.427][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-03-02 16:07:34.428][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:34.429][biodb::testThat]
biodb.TRACE[2024-03-02 16:07:34.433][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-03-02 16:07:34.435][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-03-02 16:07:34.438][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-03-02 16:07:34.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 16:07:34.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:34.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:34.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:34.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:34.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:34.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 16:07:34.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.515][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:34.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:34.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.553][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:34.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:34.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:34.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:34.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:34.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:34.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.591][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.596][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.605][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 16:07:34.688][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-03-02 16:07:34.691][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 16:07:34.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 16:07:34.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.695][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 16:07:34.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 16:07:34.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.700][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 16:07:34.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 16:07:34.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.705][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 16:07:34.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 16:07:34.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.746][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.787][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.792][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.796][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:34.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.828][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.829][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.831][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.847][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:34.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:34.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.852][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:34.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:34.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.857][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:34.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:34.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.861][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:34.863][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:34.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.865][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.866][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:34.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:34.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.895][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.896][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.898][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:34.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:34.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:34.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:34.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:34.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:34.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:34.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.929][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:34.930][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:34.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.932][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:34.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:34.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.948][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.962][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.963][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.965][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.981][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:34.987][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:34.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.990][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:34.995][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:34.997][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:34.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:34.999][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.008][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.014][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.015][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.017][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.023][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.025][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.027][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.048][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-03-02 16:07:35.093][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-03-02 16:07:35.094][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-03-02 16:07:35.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 16:07:35.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:35.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:35.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:35.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:35.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:35.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 16:07:35.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.157][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.162][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.167][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.172][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.242][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.247][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.256][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 16:07:35.289][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-03-02 16:07:35.315][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 16:07:35.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 16:07:35.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.320][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 16:07:35.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 16:07:35.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.328][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 16:07:35.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 16:07:35.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.332][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 16:07:35.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 16:07:35.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.348][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.387][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.392][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.397][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.436][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.437][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.439][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.455][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.459][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.464][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.469][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.470][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.472][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.473][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.505][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.507][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.509][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.533][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.538][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.539][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.542][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.571][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.572][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.574][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.603][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.605][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.607][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.636][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.638][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.640][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.655][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.657][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.659][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.665][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.666][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.669][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.675][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.683][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.689][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.690][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.692][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.698][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.699][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.701][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.707][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.709][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.711][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.717][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.718][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.720][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 16:07:35.730][biodb::testThat]
biodb.INFO [2024-03-02 16:07:35.732][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-02 16:07:35.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:35.734][biodb::testThat]
biodb.DEBUG[2024-03-02 16:07:35.737][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-03-02 16:07:35.744][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-03-02 16:07:35.748][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-03-02 16:07:35.750][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-03-02 16:07:35.752][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-03-02 16:07:35.754][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-03-02 16:07:35.756][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[2024-03-02 16:07:35.758][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 16:07:35.759][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-03-02 16:07:35.761][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-03-02 16:07:35.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 16:07:35.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:35.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:35.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:35.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:35.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:35.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 16:07:35.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.802][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.832][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.838][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.843][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.852][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:35.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 16:07:35.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 16:07:35.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:35.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:35.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:35.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:35.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:35.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 16:07:35.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:35.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:35.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.914][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.919][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-03-02 16:07:35.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 16:07:35.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 16:07:35.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 16:07:35.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.969][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 16:07:35.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 16:07:35.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.984][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 16:07:35.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 16:07:35.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:35.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 16:07:35.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:35.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.000][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:36.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:36.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.005][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:36.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:36.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.014][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:36.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-03-02 16:07:36.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 16:07:36.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 16:07:36.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 16:07:36.066][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-03-02 16:07:36.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-02 16:07:36.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-02 16:07:36.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-02 16:07:36.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-02 16:07:36.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-02 16:07:36.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-02 16:07:36.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-02 16:07:36.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-02 16:07:36.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-02 16:07:36.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-02 16:07:36.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-02 16:07:36.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-02 16:07:36.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 16:07:36.109][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.111][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-02 16:07:36.112][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:36.113][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.120][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.121][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-03-02 16:07:36.123][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:36.124][biodb::testThat]
biodb.WARN [2024-03-02 16:07:36.148][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-03-02 16:07:36.172][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-03-02 16:07:36.184][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.185][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-03-02 16:07:36.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:36.187][biodb::testThat]
biodb.TRACE[2024-03-02 16:07:36.221][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 16:07:36.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 16:07:36.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.226][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 16:07:36.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 16:07:36.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.231][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 16:07:36.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 16:07:36.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.235][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 16:07:36.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 16:07:36.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 16:07:36.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 16:07:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.285][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 16:07:36.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 16:07:36.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.290][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 16:07:36.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 16:07:36.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 16:07:36.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 16:07:36.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 16:07:36.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 16:07:36.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 16:07:36.306][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.307][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-02 16:07:36.308][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:36.309][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.318][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.319][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-02 16:07:36.321][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:36.322][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.331][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.333][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-02 16:07:36.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:36.335][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.343][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.344][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-02 16:07:36.345][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 16:07:36.346][biodb::testThat]
biodb.INFO [2024-03-02 16:07:36.353][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 16:07:36.355][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-03-02 16:07:36.356][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-03-02 16:07:36.357][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 16:07:36.358][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:36.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:36.360][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.362][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.363][FUN] Functions in observer BiodbConfig: [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 [2024-03-02 16:07:36.375][biodb::testContext]
biodb.INFO [2024-03-02 16:07:36.376][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 16:07:36.377][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-03-02 16:07:36.378][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 16:07:36.379][biodb::testContext]
biodb.INFO [2024-03-02 16:07:36.386][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 16:07:36.388][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 16:07:36.392][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 16:07:36.393][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 16:07:36.394][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 16:07:36.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.398][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 16:07:36.400][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 16:07:36.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.404][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 16:07:36.405][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 16:07:36.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.409][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 16:07:36.410][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 16:07:36.412][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 16:07:36.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.416][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 16:07:36.417][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 16:07:36.418][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 16:07:36.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.422][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 16:07:36.424][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 16:07:36.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.428][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 16:07:36.429][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 16:07:36.430][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 16:07:36.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.434][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 16:07:36.436][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 16:07:36.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.440][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 16:07:36.441][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 16:07:36.442][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 16:07:36.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.447][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 16:07:36.448][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 16:07:36.449][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 16:07:36.450][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 16:07:36.451][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 16:07:36.452][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 16:07:36.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.457][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 16:07:36.458][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 16:07:36.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.462][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 16:07:36.463][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 16:07:36.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.468][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 16:07:36.469][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 16:07:36.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.473][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 16:07:36.474][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 16:07:36.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.479][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 16:07:36.480][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 16:07:36.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.484][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 16:07:36.485][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 16:07:36.495][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 16:07:36.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.524][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 16:07:36.525][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 16:07:36.526][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 16:07:36.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.531][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 16:07:36.533][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.534][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 16:07:36.535][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.536][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:36.538][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.539][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.540][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.541][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.542][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 16:07:36.544][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:36.545][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.546][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 16:07:36.547][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:36.548][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.549][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.551][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 16:07:36.551][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 16:07:36.551][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 16:07:36.551][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 16:07:36.551][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 16:07:36.552][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 16:07:36.553][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:36.554][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:36.555][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:36.556][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:36.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:36.559][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.560][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.561][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:36.562][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:36.563][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.564][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.566][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 16:07:36.568][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.569][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 16:07:36.570][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.571][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:36.573][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.574][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.575][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.580][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.582][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 16:07:36.583][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:36.584][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.585][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 16:07:36.586][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:36.587][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.589][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.590][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 16:07:36.590][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 16:07:36.590][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 16:07:36.590][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 16:07:36.590][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 16:07:36.591][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 16:07:36.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:36.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:36.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:36.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:36.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:36.598][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.599][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.600][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:36.601][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:36.602][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.603][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.605][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 16:07:36.607][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.608][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 16:07:36.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:36.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.613][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.617][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 16:07:36.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:36.619][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.620][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 16:07:36.622][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:36.623][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.624][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.625][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.627][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 16:07:36.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:36.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:36.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:36.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:36.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:36.634][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.635][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:36.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:36.638][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.640][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.641][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 16:07:36.643][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.645][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 16:07:36.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.647][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:36.648][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.649][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.650][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.653][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 16:07:36.654][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:36.655][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.656][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 16:07:36.657][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:36.659][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.660][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:36.661][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.662][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 16:07:36.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:36.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:36.665][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:36.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:36.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:36.669][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:36.670][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.671][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:36.672][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:36.673][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:36.674][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:36.676][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 16:07:36.677][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.769][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[2024-03-02 16:07:36.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:36.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:36.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:36.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:36.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:36.790][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 16:07:36.792][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 16:07:36.795][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 16:07:36.797][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 16:07:36.800][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 16:07:36.801][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 16:07:36.803][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 16:07:36.805][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 16:07:36.808][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 16:07:36.810][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 16:07:36.812][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 16:07:36.813][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 16:07:36.815][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 16:07:36.817][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 16:07:36.819][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 16:07:36.820][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 16:07:36.822][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 16:07:36.824][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 16:07:36.825][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 16:07:36.827][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 16:07:36.829][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 16:07:36.831][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 16:07:36.832][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 16:07:36.834][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 16:07:36.836][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 16:07:36.837][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 16:07:36.839][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 16:07:36.841][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 16:07:36.842][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 16:07:36.844][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 16:07:36.846][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 16:07:36.847][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 16:07:36.849][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 16:07:36.850][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 16:07:36.852][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 16:07:36.854][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 16:07:36.856][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 16:07:36.857][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 16:07:36.859][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 16:07:36.860][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 16:07:36.862][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 16:07:36.864][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 16:07:36.865][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 16:07:36.867][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 16:07:36.869][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 16:07:36.870][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 16:07:36.872][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 16:07:36.873][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 16:07:36.875][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 16:07:36.877][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 16:07:36.878][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 16:07:36.880][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 16:07:36.881][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 16:07:36.883][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 16:07:36.885][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 16:07:36.891][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 16:07:36.892][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 16:07:36.894][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 16:07:36.901][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 16:07:36.903][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 16:07:36.904][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 16:07:36.906][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 16:07:36.907][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 16:07:36.909][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 16:07:36.911][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 16:07:36.941][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 16:07:36.943][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 16:07:36.945][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 16:07:36.946][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 16:07:36.948][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 16:07:36.950][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 16:07:36.970][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 16:07:36.972][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 16:07:36.974][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 16:07:36.975][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 16:07:36.977][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 16:07:37.003][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 16:07:37.005][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 16:07:37.006][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 16:07:37.008][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 16:07:37.009][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 16:07:37.015][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 16:07:37.017][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 16:07:37.019][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 16:07:37.021][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 16:07:37.022][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 16:07:37.023][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.025][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 16:07:37.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.152][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[2024-03-02 16:07:37.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 16:07:37.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.159][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[2024-03-02 16:07:37.162][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-03-02 16:07:37.164][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-03-02 16:07:37.166][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:37.167][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-03-02 16:07:37.168][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:37.170][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 16:07:37.175][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:37.176][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-03-02 16:07:37.178][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:37.179][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 16:07:37.180][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-03-02 16:07:37.181][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 16:07:37.182][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:37.183][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-03-02 16:07:37.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 16:07:37.186][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-03-02 16:07:37.186][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-03-02 16:07:37.186][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-03-02 16:07:37.186][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-03-02 16:07:37.186][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-03-02 16:07:37.186][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-03-02 16:07:37.186][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-03-02 16:07:37.187][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 16:07:37.188][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:37.190][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 16:07:37.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:37.192][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:37.193][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 16:07:37.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 16:07:37.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 16:07:37.196][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 16:07:37.198][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-03-02 16:07:37.198][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-03-02 16:07:37.198][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-03-02 16:07:37.198][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-03-02 16:07:37.199][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 16:07:37.200][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 16:07:37.201][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 16:07:37.202][self$setPropertyValue]
biodb.DEBUG[2024-03-02 16:07:37.204][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-03-02 16:07:37.207][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-03-02 16:07:37.209][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-03-02 16:07:37.210][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-03-02 16:07:37.212][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-03-02 16:07:37.213][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 16:07:37.214][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 16:07:37.216][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 16:07:37.218][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 16:07:37.219][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-03-02 16:07:37.220][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-03-02 16:07:37.222][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 16:07:37.223][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-03-02 16:07:37.224][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-03-02 16:07:37.225][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 16:07:37.226][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 16:07:37.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 16:07:37.229][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 16:07:37.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 16:07:37.231][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 16:07:37.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  5.730   0.345   6.185

'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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.7.0’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c 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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c test-100-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-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)