Back to Long Tests report for BioC 3.20

This page was generated on 2024-11-16 23:55 -0500 (Sat, 16 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4765
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
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 11/32HostnameOS / ArchCHECK
biodbNci 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-11-16 09:55 -0500 (Sat, 16 Nov 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_20
git_last_commit: d666b49
git_last_commit_date: 2024-10-29 11:09:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on lconway

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

raw results


Summary

Package: biodbNci
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-11-16 16:07:29 -0500 (Sat, 16 Nov 2024)
EndedAt: 2024-11-16 16:12:16 -0500 (Sat, 16 Nov 2024)
EllapsedTime: 287.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


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

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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 [2024-11-16 16:12:13.685][biodb::testContext]
biodb.INFO [2024-11-16 16:12:13.688][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-16 16:12:13.689][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-11-16 16:12:13.690][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-16 16:12:13.690][biodb::testContext]
biodb.INFO [2024-11-16 16:12:13.695][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-16 16:12:13.697][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-16 16:12:13.703][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:12:13.703][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-16 16:12:13.704][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-16 16:12:13.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.707][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-16 16:12:13.720][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-16 16:12:13.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.723][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-16 16:12:13.724][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-16 16:12:13.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.727][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-16 16:12:13.728][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-16 16:12:13.729][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-16 16:12:13.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.732][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-16 16:12:13.733][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-16 16:12:13.734][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-16 16:12:13.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.737][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-16 16:12:13.738][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-16 16:12:13.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.741][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-16 16:12:13.742][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-16 16:12:13.743][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-16 16:12:13.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.746][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-16 16:12:13.747][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-16 16:12:13.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.750][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-16 16:12:13.751][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-16 16:12:13.752][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-16 16:12:13.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.755][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-16 16:12:13.756][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-16 16:12:13.756][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-16 16:12:13.757][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-16 16:12:13.758][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-16 16:12:13.759][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-16 16:12:13.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.762][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-16 16:12:13.763][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-16 16:12:13.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.766][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-16 16:12:13.767][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-16 16:12:13.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.769][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[2024-11-16 16:12:13.770][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-16 16:12:13.770][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-16 16:12:13.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.774][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-16 16:12:13.774][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-16 16:12:13.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.778][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-16 16:12:13.778][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-16 16:12:13.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.782][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-16 16:12:13.782][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-16 16:12:13.836][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-16 16:12:13.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.840][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-16 16:12:13.841][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-16 16:12:13.842][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-16 16:12:13.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:13.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:13.847][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-16 16:12:13.876][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.895][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-16 16:12:13.896][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:13.898][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.899][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.900][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.901][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.901][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-16 16:12:13.902][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:13.903][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.904][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-16 16:12:13.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:13.906][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.906][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.907][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:12:13.907][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-16 16:12:13.907][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-16 16:12:13.907][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-16 16:12:13.907][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-16 16:12:13.908][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:12:13.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:13.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:13.911][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:13.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:13.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:13.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.914][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.915][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:13.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:13.917][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.918][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.919][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-16 16:12:13.920][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.921][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-16 16:12:13.922][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:13.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.924][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.925][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.926][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.927][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-16 16:12:13.928][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:13.929][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.930][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-16 16:12:13.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:13.931][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.933][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.933][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:12:13.933][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-16 16:12:13.933][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-16 16:12:13.933][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-16 16:12:13.933][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-16 16:12:13.934][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:12:13.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:13.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:13.937][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:13.938][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:13.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:13.939][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.940][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.941][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:13.942][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:13.942][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.943][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.944][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-16 16:12:13.946][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.947][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-16 16:12:13.947][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.948][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:13.949][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.952][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.952][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-16 16:12:13.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:13.954][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.955][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-16 16:12:13.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:13.957][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.958][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.958][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.959][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:12:13.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:13.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:13.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:13.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:13.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:13.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.965][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:13.967][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:13.968][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.968][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.969][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-16 16:12:13.971][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.972][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-16 16:12:13.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:13.974][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.975][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.976][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.977][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.978][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-16 16:12:13.979][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:13.980][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.981][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-16 16:12:13.982][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:13.982][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.984][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:13.984][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.985][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:12:13.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:13.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:13.988][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:13.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:13.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:13.990][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:13.991][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.992][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:13.993][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:13.993][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:13.994][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:13.997][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:12:13.998][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:13.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.027][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[2024-11-16 16:12:14.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.035][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[2024-11-16 16:12:14.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.071][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-16 16:12:14.075][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-16 16:12:14.076][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-16 16:12:14.077][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-16 16:12:14.079][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-16 16:12:14.080][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-16 16:12:14.081][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-16 16:12:14.082][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-16 16:12:14.083][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-16 16:12:14.085][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-16 16:12:14.086][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-16 16:12:14.087][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-16 16:12:14.088][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-16 16:12:14.089][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-16 16:12:14.091][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-16 16:12:14.092][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-16 16:12:14.093][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-16 16:12:14.095][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-16 16:12:14.096][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-16 16:12:14.097][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-16 16:12:14.098][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-16 16:12:14.099][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-16 16:12:14.100][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-16 16:12:14.102][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-16 16:12:14.104][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-16 16:12:14.106][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-16 16:12:14.108][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-16 16:12:14.110][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-16 16:12:14.112][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-16 16:12:14.114][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-16 16:12:14.115][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-16 16:12:14.117][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-16 16:12:14.119][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-16 16:12:14.120][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-16 16:12:14.122][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-16 16:12:14.124][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-16 16:12:14.125][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-16 16:12:14.126][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-16 16:12:14.128][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-16 16:12:14.129][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-16 16:12:14.130][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-16 16:12:14.131][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-16 16:12:14.132][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-16 16:12:14.134][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-16 16:12:14.135][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-16 16:12:14.136][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-16 16:12:14.138][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-16 16:12:14.139][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-16 16:12:14.140][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-16 16:12:14.142][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-16 16:12:14.143][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-16 16:12:14.144][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-16 16:12:14.145][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-16 16:12:14.147][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-16 16:12:14.148][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-16 16:12:14.149][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-16 16:12:14.150][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-16 16:12:14.152][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-16 16:12:14.153][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-16 16:12:14.154][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-16 16:12:14.155][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-16 16:12:14.156][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-16 16:12:14.158][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-16 16:12:14.159][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-16 16:12:14.160][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-16 16:12:14.162][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-16 16:12:14.163][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-16 16:12:14.164][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-16 16:12:14.166][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-16 16:12:14.167][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-16 16:12:14.168][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-16 16:12:14.170][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-16 16:12:14.171][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-16 16:12:14.172][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-16 16:12:14.173][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-16 16:12:14.175][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-16 16:12:14.176][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-16 16:12:14.177][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-16 16:12:14.178][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-16 16:12:14.180][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-16 16:12:14.181][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-16 16:12:14.183][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-16 16:12:14.184][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-16 16:12:14.189][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-16 16:12:14.190][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-16 16:12:14.193][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:12:14.194][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.196][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.220][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[2024-11-16 16:12:14.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.235][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[2024-11-16 16:12:14.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.280][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[2024-11-16 16:12:14.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:14.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:14.287][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-11-16 16:12:14.294][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-11-16 16:12:14.295][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:14.296][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-11-16 16:12:14.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:14.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:14.298][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:14.299][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-11-16 16:12:14.300][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:14.301][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:14.301][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-11-16 16:12:14.302][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:14.303][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:14.304][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-11-16 16:12:14.304][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:14.305][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-11-16 16:12:14.305][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-11-16 16:12:14.305][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-11-16 16:12:14.305][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-11-16 16:12:14.305][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-11-16 16:12:14.305][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-11-16 16:12:14.305][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-11-16 16:12:14.306][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:14.307][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:14.307][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-16 16:12:14.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:14.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:14.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:14.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:14.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:14.311][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:14.312][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-11-16 16:12:14.312][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-11-16 16:12:14.312][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-11-16 16:12:14.312][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-11-16 16:12:14.313][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:14.314][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:14.314][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:14.315][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:14.319][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-11-16 16:12:14.338][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-11-16 16:12:14.339][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-11-16 16:12:14.342][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-11-16 16:12:14.346][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-11-16 16:12:14.349][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-16 16:12:14.350][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-16 16:12:14.351][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-11-16 16:12:14.352][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-11-16 16:12:14.353][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-11-16 16:12:14.354][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-11-16 16:12:14.387][biodb::testThat]
biodb.INFO [2024-11-16 16:12:14.388][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-11-16 16:12:14.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:14.390][biodb::testThat]
biodb.TRACE[2024-11-16 16:12:14.392][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-11-16 16:12:14.394][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-11-16 16:12:14.396][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-11-16 16:12:14.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:12:14.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-16 16:12:14.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.493][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.496][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.501][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:12:14.551][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-11-16 16:12:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:12:14.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:12:14.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:12:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:12:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-16 16:12:14.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-16 16:12:14.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-16 16:12:14.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-16 16:12:14.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.592][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.619][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.623][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.626][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.649][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.650][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.651][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.663][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.666][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.669][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.672][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.672][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.674][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.674][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.694][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.694][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.696][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.715][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.715][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.717][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.738][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.739][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.740][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.751][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.754][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.763][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.764][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.765][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.770][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.770][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.772][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.776][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.777][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.779][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.783][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.784][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.785][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.799][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-11-16 16:12:14.827][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-11-16 16:12:14.828][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-11-16 16:12:14.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:12:14.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:14.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:14.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:14.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:14.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:14.838][FUN] Functions in observer BiodbConfig: [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[2024-11-16 16:12:14.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.864][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:14.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:14.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.872][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:14.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:14.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.878][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:14.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:14.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:14.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:14.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:14.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:14.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:14.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:14.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:14.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:14.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:14.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:14.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:14.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:14.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:14.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:14.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:14.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:14.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.917][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:14.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.926][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.932][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:12:14.954][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-11-16 16:12:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:12:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:12:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.974][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:12:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:12:14.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.977][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-16 16:12:14.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-16 16:12:14.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.984][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-16 16:12:14.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-16 16:12:14.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:14.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:14.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:14.994][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:14.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:14.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.021][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.024][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.027][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.052][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.053][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.054][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.065][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.068][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.071][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.074][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.075][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.076][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.077][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.096][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.096][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.102][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.113][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.119][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.122][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.123][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.124][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.125][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.144][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.144][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.146][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.165][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.166][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.168][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.187][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.188][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.189][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.200][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.203][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.207][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.208][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.209][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.214][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.215][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.216][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.220][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.226][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.227][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.231][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.232][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.234][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.238][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.239][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.240][ef$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.245][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.246][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.248][ef$get] fields variable is a list.
biodb.INFO [2024-11-16 16:12:15.255][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.256][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-16 16:12:15.257][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:15.257][biodb::testThat]
biodb.DEBUG[2024-11-16 16:12:15.259][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-11-16 16:12:15.264][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-11-16 16:12:15.268][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-11-16 16:12:15.269][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-11-16 16:12:15.271][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-11-16 16:12:15.272][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-11-16 16:12:15.274][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[2024-11-16 16:12:15.275][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-11-16 16:12:15.276][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-11-16 16:12:15.276][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-11-16 16:12:15.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:12:15.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:15.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:15.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-16 16:12:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.302][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.317][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.324][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.326][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.332][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:12:15.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-16 16:12:15.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:15.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:15.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-16 16:12:15.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.370][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.373][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-16 16:12:15.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.376][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-16 16:12:15.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-16 16:12:15.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-16 16:12:15.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-16 16:12:15.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-16 16:12:15.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-16 16:12:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-16 16:12:15.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-16 16:12:15.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.422][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.425][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.431][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-11-16 16:12:15.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-16 16:12:15.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-16 16:12:15.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-16 16:12:15.464][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-11-16 16:12:15.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-16 16:12:15.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-16 16:12:15.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-16 16:12:15.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-16 16:12:15.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-16 16:12:15.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-16 16:12:15.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-16 16:12:15.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-16 16:12:15.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-16 16:12:15.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-16 16:12:15.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-16 16:12:15.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-16 16:12:15.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-16 16:12:15.495][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.495][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-16 16:12:15.496][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:15.497][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.502][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.503][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-11-16 16:12:15.503][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:15.504][biodb::testThat]
biodb.WARN [2024-11-16 16:12:15.518][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-11-16 16:12:15.533][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-11-16 16:12:15.541][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.542][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-11-16 16:12:15.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:15.544][biodb::testThat]
biodb.TRACE[2024-11-16 16:12:15.562][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:12:15.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:12:15.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:12:15.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:12:15.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.568][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-16 16:12:15.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-16 16:12:15.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.576][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-16 16:12:15.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-16 16:12:15.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.601][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:12:15.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:12:15.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.605][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-16 16:12:15.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-16 16:12:15.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.607][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-16 16:12:15.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-16 16:12:15.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-16 16:12:15.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-16 16:12:15.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-16 16:12:15.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-16 16:12:15.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-16 16:12:15.619][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.620][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-16 16:12:15.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:15.622][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.629][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.629][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-16 16:12:15.630][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:15.631][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.638][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.639][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-16 16:12:15.639][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:15.640][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.646][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.647][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-16 16:12:15.648][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-16 16:12:15.648][biodb::testThat]
biodb.INFO [2024-11-16 16:12:15.654][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-16 16:12:15.655][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-11-16 16:12:15.656][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-11-16 16:12:15.656][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-16 16:12:15.657][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:15.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:15.658][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.660][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-16 16:12:15.667][biodb::testContext]
biodb.INFO [2024-11-16 16:12:15.668][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-16 16:12:15.669][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-11-16 16:12:15.669][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-16 16:12:15.670][biodb::testContext]
biodb.INFO [2024-11-16 16:12:15.672][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-16 16:12:15.673][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-16 16:12:15.676][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:12:15.677][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-16 16:12:15.678][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-16 16:12:15.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.685][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-16 16:12:15.685][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-16 16:12:15.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.688][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-16 16:12:15.689][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-16 16:12:15.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.691][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-16 16:12:15.692][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-16 16:12:15.693][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-16 16:12:15.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.695][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-16 16:12:15.696][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-16 16:12:15.697][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-16 16:12:15.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.699][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-16 16:12:15.700][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-16 16:12:15.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.703][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-16 16:12:15.704][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-16 16:12:15.704][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-16 16:12:15.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.707][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-16 16:12:15.708][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-16 16:12:15.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.710][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-16 16:12:15.711][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-16 16:12:15.712][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-16 16:12:15.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.715][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-16 16:12:15.715][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-16 16:12:15.716][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-16 16:12:15.717][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-16 16:12:15.718][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-16 16:12:15.718][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-16 16:12:15.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.721][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-16 16:12:15.722][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-16 16:12:15.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.724][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-16 16:12:15.725][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-16 16:12:15.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.728][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-16 16:12:15.729][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-16 16:12:15.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.731][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-16 16:12:15.732][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-16 16:12:15.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.735][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-16 16:12:15.736][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-16 16:12:15.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.738][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-16 16:12:15.739][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-16 16:12:15.756][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-16 16:12:15.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.759][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-16 16:12:15.760][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-16 16:12:15.761][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-16 16:12:15.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.764][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-16 16:12:15.765][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.766][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-16 16:12:15.766][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.767][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:15.768][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.769][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.769][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.770][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.771][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-16 16:12:15.772][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:15.772][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.773][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-16 16:12:15.774][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:15.774][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.775][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.776][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:12:15.776][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-16 16:12:15.776][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-16 16:12:15.776][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-16 16:12:15.776][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-16 16:12:15.777][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:12:15.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:15.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:15.779][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:15.780][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:15.780][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:15.781][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.782][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.782][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:15.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:15.784][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.784][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.785][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-16 16:12:15.787][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.787][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-16 16:12:15.788][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.789][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:15.789][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.790][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.791][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.792][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.792][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-16 16:12:15.793][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:15.794][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.795][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-16 16:12:15.795][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:15.796][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.797][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.798][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-16 16:12:15.798][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-16 16:12:15.798][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-16 16:12:15.798][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-16 16:12:15.798][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-16 16:12:15.799][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:12:15.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:15.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:15.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:15.805][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:15.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:15.807][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.807][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:15.809][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:15.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.810][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.811][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-16 16:12:15.812][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.813][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-16 16:12:15.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:15.815][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.816][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.816][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.817][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.818][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-16 16:12:15.819][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:15.819][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.820][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-16 16:12:15.821][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:15.822][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.822][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.823][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.824][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:12:15.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:15.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:15.826][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:15.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:15.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:15.828][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.829][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.829][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:15.830][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:15.831][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.831][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.832][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-16 16:12:15.834][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.834][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-16 16:12:15.835][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.836][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:15.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.837][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.838][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.839][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.839][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-16 16:12:15.840][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:15.841][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.842][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-16 16:12:15.842][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:15.843][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.844][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:15.845][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.845][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-16 16:12:15.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:15.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:15.847][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:15.848][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:15.849][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:15.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:15.850][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:15.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:15.852][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:15.853][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:15.854][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:12:15.855][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:15.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:15.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:15.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:15.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:15.915][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-16 16:12:15.916][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-16 16:12:15.918][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-16 16:12:15.919][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-16 16:12:15.920][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-16 16:12:15.921][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-16 16:12:15.922][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-16 16:12:15.923][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-16 16:12:15.924][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-16 16:12:15.925][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-16 16:12:15.926][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-16 16:12:15.927][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-16 16:12:15.928][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-16 16:12:15.929][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-16 16:12:15.930][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-16 16:12:15.931][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-16 16:12:15.932][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-16 16:12:15.933][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-16 16:12:15.934][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-16 16:12:15.935][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-16 16:12:15.936][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-16 16:12:15.937][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-16 16:12:15.938][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-16 16:12:15.939][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-16 16:12:15.940][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-16 16:12:15.941][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-16 16:12:15.942][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-16 16:12:15.943][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-16 16:12:15.944][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-16 16:12:15.945][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-16 16:12:15.946][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-16 16:12:15.947][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-16 16:12:15.948][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-16 16:12:15.949][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-16 16:12:15.950][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-16 16:12:15.951][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-16 16:12:15.952][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-16 16:12:15.953][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-16 16:12:15.954][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-16 16:12:15.955][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-16 16:12:15.956][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-16 16:12:15.957][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-16 16:12:15.958][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-16 16:12:15.959][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-16 16:12:15.960][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-16 16:12:15.961][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-16 16:12:15.962][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-16 16:12:15.963][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-16 16:12:15.964][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-16 16:12:15.965][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-16 16:12:15.966][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-16 16:12:15.967][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-16 16:12:15.969][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-16 16:12:15.970][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-16 16:12:15.971][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-16 16:12:15.972][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-16 16:12:15.973][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-16 16:12:15.974][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-16 16:12:15.975][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-16 16:12:15.976][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-16 16:12:15.977][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-16 16:12:15.978][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-16 16:12:15.979][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-16 16:12:15.980][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-16 16:12:15.981][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-16 16:12:15.982][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-16 16:12:15.983][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-16 16:12:15.984][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-16 16:12:15.985][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-16 16:12:15.986][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-16 16:12:15.987][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-16 16:12:15.988][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-16 16:12:15.989][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-16 16:12:15.990][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-16 16:12:15.991][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-16 16:12:15.992][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-16 16:12:15.993][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-16 16:12:15.994][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-16 16:12:15.995][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-16 16:12:15.996][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-16 16:12:15.997][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-16 16:12:15.998][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-16 16:12:15.999][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-16 16:12:16.000][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-16 16:12:16.006][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-16 16:12:16.006][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-16 16:12:16.007][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.009][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-16 16:12:16.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-16 16:12:16.089][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-11-16 16:12:16.090][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-11-16 16:12:16.092][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:16.092][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-11-16 16:12:16.093][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:16.094][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-16 16:12:16.095][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:16.095][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-11-16 16:12:16.096][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:16.097][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-16 16:12:16.098][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-11-16 16:12:16.098][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-16 16:12:16.099][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:16.100][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-11-16 16:12:16.100][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-16 16:12:16.101][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-11-16 16:12:16.101][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-11-16 16:12:16.101][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-11-16 16:12:16.101][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-11-16 16:12:16.101][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-11-16 16:12:16.101][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-11-16 16:12:16.101][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-11-16 16:12:16.102][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-16 16:12:16.103][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:16.103][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-16 16:12:16.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:16.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:16.109][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-16 16:12:16.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-16 16:12:16.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-16 16:12:16.111][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-16 16:12:16.112][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-11-16 16:12:16.112][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-11-16 16:12:16.112][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-11-16 16:12:16.112][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-11-16 16:12:16.113][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-16 16:12:16.113][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-16 16:12:16.114][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-16 16:12:16.115][self$setPropertyValue]
biodb.DEBUG[2024-11-16 16:12:16.116][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-11-16 16:12:16.118][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-11-16 16:12:16.119][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-11-16 16:12:16.119][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-11-16 16:12:16.120][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-11-16 16:12:16.121][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-16 16:12:16.122][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-16 16:12:16.123][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-11-16 16:12:16.124][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-11-16 16:12:16.125][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-11-16 16:12:16.126][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-11-16 16:12:16.126][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-16 16:12:16.127][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-11-16 16:12:16.128][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-11-16 16:12:16.129][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-16 16:12:16.129][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-16 16:12:16.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-16 16:12:16.131][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-16 16:12:16.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-16 16:12:16.132][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-16 16:12:16.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  3.691   0.279   4.054

'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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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-3.20-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)