Back to Long Tests report for BioC 3.19

This page was generated on 2024-07-13 23:55 -0400 (Sat, 13 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 12/33HostnameOS / ArchCHECK
biodbNci 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-13 09:55 -0400 (Sat, 13 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_19
git_last_commit: 0db4525
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.4 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1

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

raw results


Summary

Package: biodbNci
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-07-13 16:02:40 -0400 (Sat, 13 Jul 2024)
EndedAt: 2024-07-13 16:04:03 -0400 (Sat, 13 Jul 2024)
EllapsedTime: 82.7 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-07-13 16:03:57.916][biodb::testContext]
biodb.INFO [2024-07-13 16:03:57.920][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:03:57.921][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-13 16:03:57.922][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:03:57.923][biodb::testContext]
biodb.INFO [2024-07-13 16:03:57.931][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:03:57.933][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-13 16:03:57.941][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:03:57.942][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-13 16:03:57.944][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-13 16:03:57.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:57.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:57.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:57.948][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-13 16:03:57.977][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-13 16:03:57.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:57.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:57.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:57.983][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-13 16:03:57.985][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-13 16:03:57.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:57.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:57.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:57.990][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-13 16:03:57.991][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-13 16:03:57.993][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-13 16:03:57.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:57.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:57.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:57.997][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-13 16:03:57.998][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-13 16:03:58.000][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-13 16:03:58.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.004][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-13 16:03:58.006][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-13 16:03:58.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.010][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-13 16:03:58.011][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-13 16:03:58.013][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-13 16:03:58.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.017][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-13 16:03:58.018][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-13 16:03:58.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.023][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-13 16:03:58.024][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-13 16:03:58.025][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-13 16:03:58.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.030][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:03:58.031][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-13 16:03:58.032][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-13 16:03:58.034][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-13 16:03:58.035][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-13 16:03:58.036][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-13 16:03:58.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.039][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[2024-07-13 16:03:58.041][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-13 16:03:58.042][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-13 16:03:58.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.046][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-13 16:03:58.048][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-13 16:03:58.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.052][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-13 16:03:58.054][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-13 16:03:58.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.058][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-13 16:03:58.059][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:03:58.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.064][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-13 16:03:58.065][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-13 16:03:58.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.070][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:03:58.071][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-13 16:03:58.081][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-13 16:03:58.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.086][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-13 16:03:58.087][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-13 16:03:58.088][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-13 16:03:58.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.095][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-13 16:03:58.140][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.168][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-13 16:03:58.170][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.171][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:58.172][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.174][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.175][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.176][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.177][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:03:58.179][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:58.180][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.181][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-13 16:03:58.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:58.184][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.185][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.186][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:03:58.186][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:03:58.186][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:03:58.186][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:03:58.186][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:03:58.188][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:03:58.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:58.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.195][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.196][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.197][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:58.198][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:58.199][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.201][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.202][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-13 16:03:58.204][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.206][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:03:58.207][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.208][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:58.209][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.211][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.212][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.213][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.214][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:03:58.216][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:58.217][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.218][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-13 16:03:58.219][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:58.221][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.222][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.223][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:03:58.223][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:03:58.223][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:03:58.223][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:03:58.223][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:03:58.225][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:03:58.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.228][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:58.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.232][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.233][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.234][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:58.235][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:58.236][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.238][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.239][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-13 16:03:58.241][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.243][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-13 16:03:58.244][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.245][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:58.246][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.248][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.249][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.250][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.251][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:03:58.253][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:58.254][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.255][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-13 16:03:58.257][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:58.258][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.259][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.260][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.261][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:03:58.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.265][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:58.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.270][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:58.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:58.273][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.275][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.276][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-13 16:03:58.278][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.280][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:03:58.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.282][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:58.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.285][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.286][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.287][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.288][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:03:58.290][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:58.291][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.292][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-13 16:03:58.294][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:58.295][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.296][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.297][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.299][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:03:58.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.302][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:58.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.306][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.307][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.308][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:58.309][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:58.311][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.312][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.317][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:03:58.318][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.330][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[2024-07-13 16:03:58.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.336][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[2024-07-13 16:03:58.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.342][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[2024-07-13 16:03:58.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.421][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-13 16:03:58.426][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-13 16:03:58.428][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-13 16:03:58.430][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-13 16:03:58.431][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-13 16:03:58.433][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:03:58.435][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-13 16:03:58.437][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-13 16:03:58.438][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:03:58.440][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:03:58.442][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:03:58.443][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-13 16:03:58.445][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-13 16:03:58.447][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-13 16:03:58.449][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-13 16:03:58.450][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:03:58.452][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-13 16:03:58.454][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-13 16:03:58.455][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-13 16:03:58.457][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-13 16:03:58.459][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-13 16:03:58.461][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-13 16:03:58.462][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-13 16:03:58.464][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-13 16:03:58.466][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-13 16:03:58.467][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-13 16:03:58.469][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-13 16:03:58.471][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-13 16:03:58.473][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-13 16:03:58.474][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-13 16:03:58.476][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-13 16:03:58.478][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-13 16:03:58.479][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-13 16:03:58.481][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-13 16:03:58.483][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-13 16:03:58.485][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-13 16:03:58.486][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-13 16:03:58.488][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-13 16:03:58.490][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-13 16:03:58.491][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-13 16:03:58.493][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-13 16:03:58.495][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-13 16:03:58.497][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-13 16:03:58.498][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-13 16:03:58.500][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-13 16:03:58.502][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-13 16:03:58.503][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-13 16:03:58.505][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-13 16:03:58.507][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-13 16:03:58.509][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-13 16:03:58.510][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-13 16:03:58.512][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-13 16:03:58.514][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-13 16:03:58.515][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-13 16:03:58.517][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-13 16:03:58.519][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-13 16:03:58.521][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-13 16:03:58.522][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-13 16:03:58.524][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-13 16:03:58.526][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-13 16:03:58.528][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-13 16:03:58.529][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-13 16:03:58.531][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-13 16:03:58.533][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-13 16:03:58.534][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-13 16:03:58.536][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-13 16:03:58.538][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-13 16:03:58.540][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-13 16:03:58.541][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-13 16:03:58.543][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-13 16:03:58.545][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-13 16:03:58.547][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-13 16:03:58.548][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-13 16:03:58.550][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-13 16:03:58.552][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-13 16:03:58.554][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-13 16:03:58.555][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-13 16:03:58.557][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-13 16:03:58.559][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-13 16:03:58.560][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-13 16:03:58.562][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-13 16:03:58.564][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-13 16:03:58.566][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-13 16:03:58.573][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-13 16:03:58.575][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:03:58.579][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:03:58.580][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.582][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.609][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[2024-07-13 16:03:58.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.655][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[2024-07-13 16:03:58.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.686][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[2024-07-13 16:03:58.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:58.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:58.728][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-07-13 16:03:58.741][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-07-13 16:03:58.743][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.744][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-07-13 16:03:58.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.747][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:58.748][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.749][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-07-13 16:03:58.751][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.752][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.753][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-07-13 16:03:58.754][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:58.755][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.757][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-07-13 16:03:58.758][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:58.759][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-07-13 16:03:58.759][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-07-13 16:03:58.759][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-07-13 16:03:58.759][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-07-13 16:03:58.759][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-07-13 16:03:58.759][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-07-13 16:03:58.759][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-07-13 16:03:58.761][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:58.762][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.763][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-13 16:03:58.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:58.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:58.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:58.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:58.771][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-13 16:03:58.771][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-13 16:03:58.771][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-07-13 16:03:58.771][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-07-13 16:03:58.773][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:58.774][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:58.775][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:58.776][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:58.784][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-07-13 16:03:58.809][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-07-13 16:03:58.811][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-07-13 16:03:58.815][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-07-13 16:03:58.820][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-07-13 16:03:58.825][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:03:58.827][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:03:58.828][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:03:58.830][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:03:58.832][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:03:58.833][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-07-13 16:03:58.874][biodb::testThat]
biodb.INFO [2024-07-13 16:03:58.875][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-13 16:03:58.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:03:58.878][biodb::testThat]
biodb.TRACE[2024-07-13 16:03:58.882][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-07-13 16:03:58.884][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-07-13 16:03:58.888][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-07-13 16:03:58.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:03:58.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:58.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:58.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:58.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:58.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:58.920][FUN] Functions in observer BiodbConfig: [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[2024-07-13 16:03:58.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:58.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:58.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:58.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:58.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:58.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:58.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:58.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:58.969][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:58.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:58.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:58.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.047][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.052][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.062][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:03:59.148][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-07-13 16:03:59.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:03:59.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:03:59.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.156][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:03:59.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:03:59.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.161][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:03:59.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:03:59.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.166][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:03:59.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:03:59.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.209][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.251][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.256][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.261][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.293][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.295][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.297][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.318][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.327][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.331][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.361][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.363][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.365][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.395][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.397][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.399][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.431][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.434][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.450][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.451][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.453][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.464][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.465][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.467][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.473][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.475][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.477][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.485][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.487][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.493][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.494][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.497][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.519][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-07-13 16:03:59.567][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-07-13 16:03:59.569][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-07-13 16:03:59.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:03:59.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:59.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:59.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:59.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:59.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:59.583][FUN] Functions in observer BiodbConfig: [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[2024-07-13 16:03:59.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.632][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.641][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.647][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:59.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:59.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:03:59.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.689][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:59.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:59.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:59.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.727][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.732][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.742][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:03:59.777][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-07-13 16:03:59.806][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:03:59.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:03:59.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:03:59.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:03:59.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.816][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:03:59.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:03:59.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:03:59.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:03:59.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.841][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.883][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.888][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.893][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:03:59.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.936][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.937][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.939][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:59.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:59.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.956][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.961][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.966][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.971][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.972][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.974][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.975][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:59.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:59.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:59.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:59.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.005][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.007][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.028][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.043][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.044][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.047][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.077][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.078][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.080][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.111][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.112][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.114][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.145][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.146][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.148][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.164][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.168][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.174][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:04:00.175][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:04:00.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.178][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.184][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.185][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.187][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.194][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.197][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.207][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.208][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.211][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.217][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.218][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.220][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.227][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.228][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.230][ef$get] fields variable is a list.
biodb.INFO [2024-07-13 16:04:00.240][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.241][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-13 16:04:00.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:00.244][biodb::testThat]
biodb.DEBUG[2024-07-13 16:04:00.246][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-07-13 16:04:00.254][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-07-13 16:04:00.259][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-07-13 16:04:00.261][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-07-13 16:04:00.263][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-07-13 16:04:00.265][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-13 16:04:00.267][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[2024-07-13 16:04:00.268][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-07-13 16:04:00.270][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-07-13 16:04:00.271][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-07-13 16:04:00.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:04:00.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:00.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:00.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:00.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:00.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-13 16:04:00.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.307][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.350][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.355][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.365][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:00.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:04:00.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:00.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:00.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:00.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:00.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-13 16:04:00.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:04:00.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:04:00.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.434][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:04:00.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:04:00.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.439][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.444][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:04:00.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:04:00.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-13 16:04:00.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:00.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:00.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.496][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:04:00.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:04:00.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:04:00.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.518][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.523][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.532][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-07-13 16:04:00.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:00.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:00.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:00.582][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-07-13 16:04:00.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-13 16:04:00.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-13 16:04:00.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:04:00.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:04:00.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:04:00.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:04:00.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-13 16:04:00.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-13 16:04:00.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:04:00.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:04:00.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:04:00.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:04:00.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-13 16:04:00.631][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.632][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-13 16:04:00.633][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:00.635][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.642][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.644][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-13 16:04:00.645][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:00.646][biodb::testThat]
biodb.WARN [2024-07-13 16:04:00.672][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-07-13 16:04:00.698][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-07-13 16:04:00.710][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.711][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-13 16:04:00.712][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:00.713][biodb::testThat]
biodb.TRACE[2024-07-13 16:04:00.745][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:00.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:00.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.750][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:00.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:00.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.755][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:00.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:00.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.760][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:00.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:00.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.815][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:00.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:00.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.820][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:00.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:00.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.825][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:00.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:00.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:00.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:00.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:00.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:00.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-13 16:04:00.842][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.844][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-13 16:04:00.845][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:00.846][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.855][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.856][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-13 16:04:00.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:00.859][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.868][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.869][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-13 16:04:00.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:00.872][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.880][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.881][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-13 16:04:00.882][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:00.883][biodb::testThat]
biodb.INFO [2024-07-13 16:04:00.891][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-13 16:04:00.892][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-07-13 16:04:00.893][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-07-13 16:04:00.894][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-13 16:04:00.896][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:00.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:00.898][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:00.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:00.900][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-13 16:04:00.913][biodb::testContext]
biodb.INFO [2024-07-13 16:04:00.914][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:04:00.916][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-07-13 16:04:00.917][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:04:00.918][biodb::testContext]
biodb.INFO [2024-07-13 16:04:00.920][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:04:00.922][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-13 16:04:00.926][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:00.928][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-13 16:04:00.929][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-13 16:04:00.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.933][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-13 16:04:00.934][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-13 16:04:00.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.943][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-13 16:04:00.945][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-13 16:04:00.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.949][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-13 16:04:00.950][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-13 16:04:00.951][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-13 16:04:00.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.956][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-13 16:04:00.957][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-13 16:04:00.958][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-13 16:04:00.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.963][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-13 16:04:00.964][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-13 16:04:00.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.968][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-13 16:04:00.970][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-13 16:04:00.971][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-13 16:04:00.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.975][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-13 16:04:00.977][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-13 16:04:00.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.981][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-13 16:04:00.982][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-13 16:04:00.984][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-13 16:04:00.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.988][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:04:00.989][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-13 16:04:00.991][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-13 16:04:00.992][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-13 16:04:00.993][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-13 16:04:00.994][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-13 16:04:00.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:00.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:00.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:00.999][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-13 16:04:01.000][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-13 16:04:01.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.004][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-13 16:04:01.006][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-13 16:04:01.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.010][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-13 16:04:01.011][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-13 16:04:01.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.016][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-13 16:04:01.017][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:04:01.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.022][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-13 16:04:01.023][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-13 16:04:01.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.028][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:04:01.029][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-13 16:04:01.039][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-13 16:04:01.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.044][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-13 16:04:01.045][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-13 16:04:01.046][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-13 16:04:01.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.051][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-13 16:04:01.053][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.054][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-13 16:04:01.056][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.057][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:01.058][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.059][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.061][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.062][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.063][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:04:01.064][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:01.066][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.067][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-13 16:04:01.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:01.069][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.070][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.072][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:04:01.072][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:04:01.072][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:04:01.072][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:04:01.072][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:04:01.073][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:01.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.077][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:01.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.080][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.081][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:01.084][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:01.085][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.086][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.088][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-13 16:04:01.090][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.091][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:04:01.092][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.094][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:01.095][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.096][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.097][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.099][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.100][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:04:01.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:01.102][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.104][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-13 16:04:01.105][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:01.106][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.107][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.109][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:04:01.109][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:04:01.109][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:04:01.109][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:04:01.109][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:04:01.110][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:01.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.113][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:01.115][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.117][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.118][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.124][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:01.125][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:01.126][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.127][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.129][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-13 16:04:01.131][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.132][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-13 16:04:01.133][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.134][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:01.136][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.137][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.138][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.139][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.141][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:04:01.142][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:01.143][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.144][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-13 16:04:01.146][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:01.147][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.148][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.149][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.151][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:01.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.154][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:01.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.158][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.159][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.160][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:01.161][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:01.162][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.164][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.165][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-13 16:04:01.167][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.169][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:04:01.170][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.171][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:01.172][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.174][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.175][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.176][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.177][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:04:01.179][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:01.180][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.181][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-13 16:04:01.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:01.183][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.185][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.186][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.187][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:01.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:01.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.194][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.195][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.197][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:01.198][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:01.199][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.200][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.202][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:01.203][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.305][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-13 16:04:01.307][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-13 16:04:01.308][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-13 16:04:01.310][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-13 16:04:01.312][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-13 16:04:01.314][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:04:01.316][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-13 16:04:01.317][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-13 16:04:01.319][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:04:01.321][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:04:01.323][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:04:01.324][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-13 16:04:01.326][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-13 16:04:01.328][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-13 16:04:01.330][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-13 16:04:01.331][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:04:01.333][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-13 16:04:01.335][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-13 16:04:01.337][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-13 16:04:01.338][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-13 16:04:01.340][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-13 16:04:01.342][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-13 16:04:01.343][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-13 16:04:01.345][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-13 16:04:01.347][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-13 16:04:01.349][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-13 16:04:01.350][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-13 16:04:01.352][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-13 16:04:01.354][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-13 16:04:01.356][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-13 16:04:01.358][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-13 16:04:01.360][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-13 16:04:01.362][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-13 16:04:01.363][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-13 16:04:01.365][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-13 16:04:01.367][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-13 16:04:01.368][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-13 16:04:01.370][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-13 16:04:01.372][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-13 16:04:01.374][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-13 16:04:01.376][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-13 16:04:01.377][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-13 16:04:01.379][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-13 16:04:01.381][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-13 16:04:01.383][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-13 16:04:01.384][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-13 16:04:01.386][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-13 16:04:01.388][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-13 16:04:01.390][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-13 16:04:01.391][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-13 16:04:01.393][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-13 16:04:01.395][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-13 16:04:01.396][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-13 16:04:01.398][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-13 16:04:01.400][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-13 16:04:01.402][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-13 16:04:01.403][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-13 16:04:01.405][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-13 16:04:01.407][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-13 16:04:01.408][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-13 16:04:01.410][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-13 16:04:01.412][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-13 16:04:01.413][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-13 16:04:01.415][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-13 16:04:01.417][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-13 16:04:01.419][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-13 16:04:01.420][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-13 16:04:01.422][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-13 16:04:01.424][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-13 16:04:01.425][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-13 16:04:01.427][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-13 16:04:01.429][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-13 16:04:01.431][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-13 16:04:01.432][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-13 16:04:01.434][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-13 16:04:01.436][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-13 16:04:01.438][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-13 16:04:01.440][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-13 16:04:01.442][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-13 16:04:01.443][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-13 16:04:01.445][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-13 16:04:01.447][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-13 16:04:01.448][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-13 16:04:01.450][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-13 16:04:01.452][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:04:01.453][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:01.454][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.457][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:01.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:01.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.593][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[2024-07-13 16:04:01.596][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-07-13 16:04:01.598][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-07-13 16:04:01.600][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.601][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-07-13 16:04:01.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.604][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:01.605][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.606][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-07-13 16:04:01.608][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.609][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.610][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-07-13 16:04:01.611][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:01.613][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.614][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-07-13 16:04:01.616][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:01.617][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-07-13 16:04:01.617][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-07-13 16:04:01.617][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-07-13 16:04:01.617][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-07-13 16:04:01.617][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-07-13 16:04:01.617][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-07-13 16:04:01.617][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-07-13 16:04:01.619][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:01.620][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.622][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-13 16:04:01.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:01.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:01.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:01.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:01.630][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-13 16:04:01.630][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-07-13 16:04:01.630][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-07-13 16:04:01.630][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-07-13 16:04:01.635][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:01.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:01.638][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:01.639][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:01.641][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-07-13 16:04:01.645][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-07-13 16:04:01.646][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-07-13 16:04:01.647][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-07-13 16:04:01.649][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-07-13 16:04:01.651][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:04:01.652][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:04:01.653][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:04:01.655][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:04:01.656][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-07-13 16:04:01.658][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-07-13 16:04:01.659][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-13 16:04:01.660][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-07-13 16:04:01.662][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-07-13 16:04:01.663][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-13 16:04:01.664][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:01.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:01.666][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:01.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:01.668][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:01.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  5.740   0.325   6.051

'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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-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 12.7.5
* 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 ‘1.8.0’
* 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-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)