Back to Long Tests report for BioC 3.20

This page was generated on 2024-07-06 23:55 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
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 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-06 09:55 -0400 (Sat, 06 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 12acfea
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino6Windows Server 2022 Datacenter / x64  OK  
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: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2024-07-06 16:03:34 -0400 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 16:27:08 -0400 (Sat, 06 Jul 2024)
EllapsedTime: 1413.2 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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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> # 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 [2024-07-06 16:04:23.573][biodb::testContext]
biodb.INFO [2024-07-06 16:04:23.576][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:04:23.576][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-06 16:04:23.577][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:04:23.578][biodb::testContext]
biodb.INFO [2024-07-06 16:04:23.583][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:04:23.584][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:04:23.590][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:04:23.590][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:04:23.591][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:04:23.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.594][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:04:23.607][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:04:23.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.610][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:04:23.611][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:04:23.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.614][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:04:23.615][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:04:23.615][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:04:23.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.618][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:04:23.619][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:04:23.620][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:04:23.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.622][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:04:23.623][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:04:23.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.626][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:04:23.627][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:04:23.628][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:04:23.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.631][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:04:23.631][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:04:23.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.634][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:04:23.635][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:04:23.635][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:04:23.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.638][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:04:23.639][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:04:23.639][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:04:23.641][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:04:23.641][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:04:23.642][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:04:23.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.645][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:04:23.646][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:04:23.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.649][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:04:23.649][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:04:23.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.652][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:04:23.653][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:04:23.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.655][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:04:23.656][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:04:23.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.659][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:04:23.659][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:04:23.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.662][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:04:23.663][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:04:23.679][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:04:23.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.682][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:04:23.683][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:04:23.684][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:04:23.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.689][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:04:23.713][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.730][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-06 16:04:23.731][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.732][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:04:23.733][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.734][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.734][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.735][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.736][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:04:23.737][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:04:23.737][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.738][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:04:23.739][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:04:23.740][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.741][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:04:23.741][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:04:23.741][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:04:23.741][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:04:23.741][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:04:23.742][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:04:23.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:23.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:23.744][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:04:23.745][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:23.746][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:23.746][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.747][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.748][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:04:23.748][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:04:23.749][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.750][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.751][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:04:23.752][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.753][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:04:23.754][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.755][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:04:23.755][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.756][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.757][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.758][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.759][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:04:23.759][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:04:23.760][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.761][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:04:23.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:04:23.762][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.764][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:04:23.764][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:04:23.764][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:04:23.764][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:04:23.764][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:04:23.765][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:04:23.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:23.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:23.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:04:23.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:23.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:23.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.770][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:04:23.771][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:04:23.772][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.773][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.773][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:04:23.775][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.775][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-06 16:04:23.776][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.777][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:04:23.778][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.779][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.780][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.780][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:04:23.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:04:23.782][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.782][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:04:23.783][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:04:23.784][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.785][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.785][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.786][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:04:23.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:23.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:23.789][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:04:23.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:23.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:23.791][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.791][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.792][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:04:23.793][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:04:23.793][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.794][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.795][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:04:23.796][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.797][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:04:23.798][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.799][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:04:23.799][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.800][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.801][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.802][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.802][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:04:23.803][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:04:23.804][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.805][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:04:23.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:04:23.806][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.807][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:23.808][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.808][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:04:23.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:23.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:23.811][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:04:23.811][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:23.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:23.813][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:04:23.814][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.814][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:04:23.815][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:04:23.816][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:23.816][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:23.819][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:04:23.820][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.838][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.DEBUG[2024-07-06 16:04:23.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.855][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[2024-07-06 16:04:23.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.862][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[2024-07-06 16:04:23.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.865][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[2024-07-06 16:04:23.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.882][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:04:23.886][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:04:23.887][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:04:23.888][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:04:23.889][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:04:23.890][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:04:23.891][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:04:23.892][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:04:23.893][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:04:23.894][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:04:23.895][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:04:23.896][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:04:23.897][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:04:23.898][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:04:23.899][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:04:23.900][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:04:23.902][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:04:23.903][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:04:23.904][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:04:23.905][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:04:23.906][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:04:23.907][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:04:23.908][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:04:23.909][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:04:23.910][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:04:23.911][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:04:23.912][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:04:23.913][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:04:23.914][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:04:23.915][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:04:23.917][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:04:23.918][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:04:23.919][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:04:23.920][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:04:23.921][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:04:23.922][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:04:23.923][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:04:23.924][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:04:23.925][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:04:23.926][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:04:23.927][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:04:23.928][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:04:23.929][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:04:23.930][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:04:23.931][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:04:23.932][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:04:23.933][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:04:23.934][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:04:23.936][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:04:23.937][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:04:23.938][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:04:23.939][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:04:23.940][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:04:23.941][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:04:23.942][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:04:23.943][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:04:23.944][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:04:23.945][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:04:23.946][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:04:23.947][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:04:23.948][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:04:23.949][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:04:23.950][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:04:23.951][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:04:23.953][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:04:23.954][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:04:23.955][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:04:23.956][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:04:23.957][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:04:23.958][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:04:23.959][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:04:23.960][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:04:23.960][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:04:23.962][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:04:23.963][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:04:23.964][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:04:23.965][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:04:23.966][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:04:23.967][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:04:23.968][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:04:23.969][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:04:23.970][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:04:23.971][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:04:23.975][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:04:23.976][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:04:23.978][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:04:23.979][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.980][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:23.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:23.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:23.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:23.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:23.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:23.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:23.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:23.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:23.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:23.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.016][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[2024-07-06 16:04:24.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.020][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[2024-07-06 16:04:24.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.039][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[2024-07-06 16:04:24.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:04:24.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:04:24.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.066][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[2024-07-06 16:04:24.068][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-07-06 16:04:24.075][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-07-06 16:04:24.077][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:24.077][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-07-06 16:04:24.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:24.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:04:24.080][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:24.080][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-07-06 16:04:24.081][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:24.082][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:04:24.082][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-07-06 16:04:24.083][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:04:24.084][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:24.085][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-07-06 16:04:24.085][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:04:24.086][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-07-06 16:04:24.086][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-07-06 16:04:24.086][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-07-06 16:04:24.086][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-07-06 16:04:24.086][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-07-06 16:04:24.086][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-07-06 16:04:24.086][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-07-06 16:04:24.087][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:04:24.087][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:24.088][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:04:24.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:24.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:24.090][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:04:24.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:04:24.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:04:24.093][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:04:24.093][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-06 16:04:24.093][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-06 16:04:24.093][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-07-06 16:04:24.093][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-07-06 16:04:24.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:04:24.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:04:24.095][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:04:24.096][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:04:24.101][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-07-06 16:04:24.119][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-07-06 16:04:24.119][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-07-06 16:04:24.123][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-07-06 16:04:24.126][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-07-06 16:04:24.129][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:04:24.130][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:04:24.131][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:04:24.132][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:04:24.132][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:04:24.133][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-07-06 16:04:24.166][biodb::testThat]
biodb.INFO [2024-07-06 16:04:24.167][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-06 16:04:24.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:04:24.168][biodb::testThat]
biodb.TRACE[2024-07-06 16:04:24.171][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[2024-07-06 16:04:24.172][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:04:24.175][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-07-06 16:04:24.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:04:24.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.197][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:04:24.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.227][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.249][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.273][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.276][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.282][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:04:24.334][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-07-06 16:04:24.336][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:04:24.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:04:24.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.339][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:04:24.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:04:24.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.342][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:04:24.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:04:24.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.345][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:04:24.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:04:24.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.373][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.399][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.402][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.405][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.427][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.428][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.430][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.440][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.446][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.449][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.450][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.452][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.452][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.472][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.473][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.475][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.495][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.496][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.498][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.515][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.518][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.519][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.520][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.531][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.532][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.533][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.541][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.542][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.543][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.547][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.548][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.550][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.554][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.556][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.560][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.561][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.562][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.575][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[2024-07-06 16:04:24.602][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:04:24.603][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-07-06 16:04:24.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:04:24.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:24.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:24.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:24.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:24.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:24.613][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:04:24.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.641][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.649][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.653][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.656][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.703][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.706][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.713][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:04:24.736][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-07-06 16:04:24.752][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:04:24.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:04:24.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.755][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:04:24.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:04:24.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.758][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:04:24.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:04:24.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.761][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:04:24.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:04:24.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.776][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.815][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.818][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.822][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:04:24.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.853][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.854][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.855][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:24.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:24.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.867][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.870][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.874][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.877][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.878][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.879][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.880][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:04:24.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.900][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.901][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.902][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:24.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:24.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.917][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.921][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.927][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.928][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.929][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:24.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:24.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.950][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.951][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.952][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:24.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.963][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.970][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.973][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.974][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.975][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:24.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:24.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.996][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.997][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:24.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:24.998][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:24.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:25.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:25.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:25.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:25.009][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:04:25.010][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:04:25.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:25.011][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:25.016][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:04:25.017][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:04:25.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:25.018][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:25.022][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:04:25.023][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:04:25.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:25.025][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:25.029][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:04:25.030][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:04:25.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:25.031][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:25.039][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:04:25.040][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:04:25.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:25.041][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:25.045][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:25.046][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:04:25.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:25.048][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:25.052][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:25.053][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:25.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:25.054][ef$get] fields variable is a list.
biodb.INFO [2024-07-06 16:04:25.061][biodb::testThat]
biodb.INFO [2024-07-06 16:04:25.062][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-06 16:04:25.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:04:25.064][biodb::testThat]
biodb.DEBUG[2024-07-06 16:04:25.065][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-07-06 16:04:25.071][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2024-07-06 16:04:25.075][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2024-07-06 16:04:25.076][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2024-07-06 16:04:25.077][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2024-07-06 16:04:25.077][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2024-07-06 16:04:25.079][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2024-07-06 16:04:56.993][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactus8a4b1abd148fgz".
biodb.TRACE[2024-07-06 16:04:56.994][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-07-06 16:04:56.996][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-07-06 16:04:56.997][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-07-06 16:04:56.998][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2024-07-06 16:04:56.999][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker8a4b7390c5ffmarker".
biodb.TRACE[2024-07-06 16:04:57.000][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2024-07-06 16:04:57.001][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-07-06 16:04:57.002][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2024-07-06 16:04:57.003][self$download] Extract whole database of nci.cactus.
biodb.INFO [2024-07-06 16:04:57.004][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2024-07-06 16:04:57.005][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-07-06 16:05:55.324][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-07-06 16:05:55.326][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2024-07-06 16:25:31.226][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2024-07-06 16:25:31.544][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2024-07-06 16:27:02.917][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-07-06 16:27:02.918][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-07-06 16:27:02.920][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker8a4b25b7239fmarker".
biodb.TRACE[2024-07-06 16:27:02.921][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2024-07-06 16:27:02.922][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-07-06 16:27:02.923][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-07-06 16:27:02.924][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-06 16:27:02.963][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-07-06 16:27:03.076][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-07-06 16:27:03.078][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-07-06 16:27:03.079][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-07-06 16:27:03.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:27:03.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:03.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:03.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:03.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:03.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:03.142][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:27:03.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.154][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:27:03.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:27:03.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:27:03.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:27:03.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:27:03.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:27:03.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:27:03.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:27:03.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:27:03.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:27:03.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:27:03.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:27:03.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.173][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:27:03.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:27:03.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:27:03.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:27:03.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.180][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.183][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.188][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:27:03.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:27:03.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:03.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:03.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:03.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:03.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:03.207][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:27:03.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.223][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:27:03.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:27:03.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.226][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:27:03.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:27:03.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:27:03.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:27:03.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.232][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:27:03.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:27:03.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:27:03.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:27:03.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-06 16:27:03.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-06 16:27:03.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:27:03.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:27:03.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:27:03.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:27:03.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:27:03.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:27:03.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:27:03.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:27:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:27:03.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:27:03.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:27:03.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:27:03.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:27:03.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:27:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:27:03.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:27:03.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:27:03.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:27:03.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:27:03.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:27:03.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:27:03.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:27:03.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.274][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.277][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.282][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-06 16:27:03.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:27:03.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:27:03.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:27:03.311][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-07-06 16:27:03.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:27:03.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:27:03.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:27:03.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:27:03.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:27:03.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:27:03.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:27:03.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:27:03.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:27:03.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:27:03.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:27:03.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:27:03.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:27:03.340][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.341][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-06 16:27:03.341][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:27:03.342][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.347][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.348][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-06 16:27:03.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:27:03.349][biodb::testThat]
biodb.WARN [2024-07-06 16:27:03.366][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-07-06 16:27:03.380][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-07-06 16:27:03.388][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.389][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-06 16:27:03.390][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:27:03.391][biodb::testThat]
biodb.TRACE[2024-07-06 16:27:03.557][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:27:03.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:27:03.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:27:03.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:27:03.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:27:03.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:27:03.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.566][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:27:03.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:27:03.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.637][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:27:03.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:27:03.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:27:03.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:27:03.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.644][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:27:03.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:27:03.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:27:03.647][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:27:03.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:27:03.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:27:03.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:27:03.802][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.802][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-06 16:27:03.803][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:27:03.804][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.810][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.811][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-06 16:27:03.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:27:03.812][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.818][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.819][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-06 16:27:03.820][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:27:03.821][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.826][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.827][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-06 16:27:03.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:27:03.829][biodb::testThat]
biodb.INFO [2024-07-06 16:27:03.834][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:27:03.835][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-07-06 16:27:03.836][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-07-06 16:27:03.836][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:27:03.837][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:03.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:03.838][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:03.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:03.840][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:03.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-06 16:27:03.910][biodb::testContext]
biodb.INFO [2024-07-06 16:27:03.911][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:27:03.912][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-07-06 16:27:03.913][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:27:03.914][biodb::testContext]
biodb.INFO [2024-07-06 16:27:04.038][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:27:04.228][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:27:04.295][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:27:04.296][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:27:04.297][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:27:04.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.300][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:27:04.300][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:27:04.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.303][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:27:04.304][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:27:04.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.307][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:27:04.308][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:27:04.309][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:27:04.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.312][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:27:04.312][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:27:04.313][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:27:04.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.316][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:27:04.316][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:27:04.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.319][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:27:04.320][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:27:04.320][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:27:04.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.323][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:27:04.324][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:27:04.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.326][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:27:04.327][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:27:04.328][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:27:04.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.330][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:27:04.331][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:27:04.332][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:27:04.332][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:27:04.333][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:27:04.334][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:27:04.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.336][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:27:04.337][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:27:04.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.340][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:27:04.341][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:27:04.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.343][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:27:04.344][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:27:04.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.346][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:27:04.347][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:27:04.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.350][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:27:04.350][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:27:04.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.353][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:27:04.354][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:27:04.896][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:27:04.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.899][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:27:04.900][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:27:04.901][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:27:04.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.904][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:27:04.905][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.906][self$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[2024-07-06 16:27:04.907][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.908][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:27:04.908][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.910][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.911][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.912][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:27:04.912][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:27:04.913][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.914][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:27:04.915][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:27:04.916][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.916][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.917][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:27:04.917][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:27:04.917][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:27:04.917][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:27:04.917][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:27:04.918][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:27:04.918][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:04.919][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:04.920][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:27:04.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:04.921][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:04.922][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.923][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.923][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:27:04.924][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:27:04.925][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.925][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.926][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:27:04.927][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.928][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:27:04.929][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.930][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:27:04.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.932][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.932][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.933][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:27:04.934][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:27:04.935][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.935][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:27:04.936][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:27:04.937][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.937][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.938][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:27:04.938][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:27:04.938][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:27:04.938][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:27:04.938][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:27:04.939][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:27:04.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:04.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:04.941][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:27:04.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:04.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:04.943][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.944][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.945][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:27:04.945][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:27:04.946][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.947][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.948][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:27:04.949][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.950][self$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[2024-07-06 16:27:04.950][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.951][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:27:04.952][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.952][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.953][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.954][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.955][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:27:04.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:27:04.956][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.957][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:27:04.957][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:27:04.958][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.959][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.959][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.960][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:27:04.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:04.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:04.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:27:04.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:04.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:04.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.965][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:27:04.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:27:04.967][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.968][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.968][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:27:04.970][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.970][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:27:04.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:27:04.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.974][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.975][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.975][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:27:04.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:27:04.977][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.978][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:27:04.978][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:27:04.979][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.980][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:04.980][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.981][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:27:04.982][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:04.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:04.983][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:27:04.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:04.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:04.985][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:27:04.986][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.987][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:27:04.987][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:27:04.988][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:04.989][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:04.990][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:27:04.990][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:04.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:04.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:04.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:04.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:04.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:04.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:04.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:04.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.020][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[2024-07-06 16:27:05.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.023][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[2024-07-06 16:27:05.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.027][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[2024-07-06 16:27:05.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.033][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[2024-07-06 16:27:05.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.046][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[2024-07-06 16:27:05.047][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:27:05.048][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:27:05.049][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:27:05.050][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:27:05.051][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:27:05.052][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:27:05.053][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:27:05.054][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:27:05.055][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:27:05.056][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:27:05.057][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:27:05.058][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:27:05.059][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:27:05.060][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:27:05.061][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:27:05.062][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:27:05.063][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:27:05.064][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:27:05.065][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:27:05.066][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:27:05.067][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:27:05.068][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:27:05.069][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:27:05.070][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:27:05.071][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:27:05.072][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:27:05.073][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:27:05.074][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:27:05.075][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:27:05.076][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:27:05.077][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:27:05.078][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:27:05.079][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:27:05.080][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:27:05.081][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:27:05.082][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:27:05.083][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:27:05.084][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:27:05.085][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:27:05.086][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:27:05.087][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:27:05.088][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:27:05.089][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:27:05.090][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:27:05.091][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:27:05.092][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:27:05.093][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:27:05.094][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:27:05.095][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:27:05.096][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:27:05.097][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:27:05.098][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:27:05.099][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:27:05.100][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:27:05.101][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:27:05.102][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:27:05.103][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:27:05.104][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:27:05.105][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:27:05.106][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:27:05.107][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:27:05.108][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:27:05.109][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:27:05.110][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:27:05.111][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:27:05.112][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:27:05.113][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:27:05.114][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:27:05.115][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:27:05.116][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:27:05.117][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:27:05.118][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:27:05.119][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:27:05.120][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:27:05.121][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:27:05.122][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:27:05.123][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:27:05.124][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:27:05.125][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:27:05.126][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:27:05.127][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:27:05.128][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:27:05.129][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:27:05.130][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:27:05.131][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:27:05.132][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:27:05.133][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.134][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:27:05.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:27:05.342][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-07-06 16:27:05.366][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-07-06 16:27:05.367][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:05.368][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-07-06 16:27:05.369][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:05.370][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:27:05.370][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:05.371][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-07-06 16:27:05.372][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:05.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:27:05.373][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-07-06 16:27:05.374][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:27:05.375][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:05.375][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-07-06 16:27:05.376][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:27:05.377][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-07-06 16:27:05.377][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-07-06 16:27:05.377][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-07-06 16:27:05.377][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-07-06 16:27:05.377][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-07-06 16:27:05.377][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-07-06 16:27:05.377][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-07-06 16:27:05.378][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:27:05.378][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:05.379][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:27:05.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:05.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:05.381][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:27:05.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:27:05.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:27:05.383][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:27:05.384][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-06 16:27:05.384][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-06 16:27:05.384][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-07-06 16:27:05.384][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-07-06 16:27:05.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:27:05.385][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:27:05.386][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:27:05.387][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:27:05.388][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-07-06 16:27:05.390][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-07-06 16:27:05.391][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-07-06 16:27:05.392][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-07-06 16:27:05.393][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-07-06 16:27:05.394][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:27:05.394][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:27:05.395][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:27:05.396][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:27:05.397][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-06 16:27:05.398][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-07-06 16:27:05.399][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:27:05.400][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-07-06 16:27:05.400][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-07-06 16:27:05.401][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:27:05.402][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:27:05.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:27:05.403][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:27:05.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:27:05.404][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:27:05.405][FUN] Functions in observer 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 
1014.382  204.635 1363.426 

'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_1.9.0.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 12.7.1
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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)