Back to Long Tests report for BioC 3.19

This page was generated on 2024-10-12 23:55 -0400 (Sat, 12 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4529
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: 2024-10-12 09:55 -0400 (Sat, 12 Oct 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 12.7.5 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: 2024-10-12 16:03:12 -0400 (Sat, 12 Oct 2024)
EndedAt: 2024-10-12 16:04:27 -0400 (Sat, 12 Oct 2024)
EllapsedTime: 75.7 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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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-10-12 16:04:22.790][biodb::testContext]
biodb.INFO [2024-10-12 16:04:22.794][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:04:22.795][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-10-12 16:04:22.796][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:04:22.797][biodb::testContext]
biodb.INFO [2024-10-12 16:04:22.804][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:04:22.806][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:04:22.814][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:22.815][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:04:22.817][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:04:22.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.821][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:04:22.847][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:04:22.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.852][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:04:22.853][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:04:22.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.857][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:04:22.859][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:04:22.860][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:04:22.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.865][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:04:22.866][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:04:22.867][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:04:22.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.872][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:04:22.873][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:04:22.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.877][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:04:22.879][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:04:22.880][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:04:22.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.885][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:04:22.887][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:04:22.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.891][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:04:22.893][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:04:22.894][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:04:22.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.898][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:04:22.900][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:04:22.901][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:04:22.902][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:04:22.903][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:04:22.905][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:04:22.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.909][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:04:22.911][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:04:22.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.915][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:04:22.916][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:04:22.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.920][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.DEBUG[2024-10-12 16:04:22.921][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:04:22.922][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:04:22.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.927][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:04:22.928][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:04:22.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.932][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[2024-10-12 16:04:22.933][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:04:22.934][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:04:22.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.939][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:04:22.940][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:04:22.951][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:04:22.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.955][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:04:22.957][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:04:22.958][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:04:22.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:22.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:22.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:22.965][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:04:23.011][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.039][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-12 16:04:23.040][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.042][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:23.043][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.044][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.045][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.047][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.048][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:04:23.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:23.050][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.052][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:04:23.053][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:23.054][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.056][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.057][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:23.057][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:04:23.057][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:04:23.057][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:04:23.057][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:04:23.058][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:23.059][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.062][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:23.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.066][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.067][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.068][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:23.069][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:23.071][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.072][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.073][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:04:23.076][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.077][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:04:23.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:23.081][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.082][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.083][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.084][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.086][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:04:23.087][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:23.088][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.089][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:04:23.091][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:23.092][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.093][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.094][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:23.094][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:04:23.094][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:04:23.094][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:04:23.094][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:04:23.096][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:23.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.099][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:23.100][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.101][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.103][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.104][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.105][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:23.106][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:23.107][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.109][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.110][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:04:23.112][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.113][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-12 16:04:23.115][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.116][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:23.117][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.120][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.121][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.122][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:04:23.123][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:23.125][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.126][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:04:23.127][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:23.128][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.129][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.131][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.132][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:23.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.135][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:23.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.140][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.141][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:23.142][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:23.144][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.145][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.146][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:04:23.148][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.150][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:04:23.151][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.152][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:23.154][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.155][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.156][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.157][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.159][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:04:23.160][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:23.161][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.162][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:04:23.164][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:23.165][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.166][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.167][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.169][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:23.170][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.172][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:23.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.176][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.177][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.178][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:23.179][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:23.180][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.182][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.186][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:23.187][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.255][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[2024-10-12 16:04:23.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.260][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[2024-10-12 16:04:23.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.266][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[2024-10-12 16:04:23.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.277][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[2024-10-12 16:04:23.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.283][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[2024-10-12 16:04:23.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.288][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[2024-10-12 16:04:23.289][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:04:23.295][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:04:23.297][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:04:23.298][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:04:23.300][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:04:23.302][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:04:23.304][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:04:23.306][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:04:23.307][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:04:23.309][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:04:23.311][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:04:23.312][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:04:23.314][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:04:23.316][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:04:23.318][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:04:23.319][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:04:23.321][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:04:23.323][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:04:23.325][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:04:23.326][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:04:23.328][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:04:23.330][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:04:23.331][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:04:23.333][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:04:23.335][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:04:23.337][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:04:23.338][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:04:23.340][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:04:23.342][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:04:23.344][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:04:23.346][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:04:23.347][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:04:23.349][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:04:23.351][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:04:23.352][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:04:23.354][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:04:23.356][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:04:23.358][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:04:23.359][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:04:23.361][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:04:23.363][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:04:23.364][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:04:23.366][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:04:23.368][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:04:23.370][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:04:23.371][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:04:23.373][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:04:23.375][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:04:23.377][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:04:23.378][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:04:23.380][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:04:23.382][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:04:23.384][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:04:23.385][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:04:23.387][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:04:23.389][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:04:23.391][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:04:23.392][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:04:23.394][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:04:23.396][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:04:23.398][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:04:23.399][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:04:23.401][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:04:23.403][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:04:23.405][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:04:23.406][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:04:23.408][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:04:23.410][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:04:23.411][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:04:23.413][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:04:23.415][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:04:23.417][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:04:23.418][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:04:23.420][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:04:23.422][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:04:23.424][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:04:23.425][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:04:23.427][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:04:23.429][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:04:23.431][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:04:23.432][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:04:23.434][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:04:23.436][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:04:23.444][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:04:23.446][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:04:23.449][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:23.450][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.453][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:23.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:23.597][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-10-12 16:04:23.609][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-10-12 16:04:23.612][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.613][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-10-12 16:04:23.614][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.616][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:23.617][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.618][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-10-12 16:04:23.619][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.620][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.622][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-10-12 16:04:23.623][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:23.624][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.625][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-10-12 16:04:23.626][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:23.628][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-10-12 16:04:23.628][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-10-12 16:04:23.628][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-10-12 16:04:23.628][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-10-12 16:04:23.628][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-10-12 16:04:23.628][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-10-12 16:04:23.628][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-10-12 16:04:23.629][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:23.630][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.631][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:04:23.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:23.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:23.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:23.638][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:23.639][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-10-12 16:04:23.639][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-10-12 16:04:23.639][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-10-12 16:04:23.639][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-10-12 16:04:23.641][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:23.642][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:23.643][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:23.644][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:23.652][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-10-12 16:04:23.674][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-10-12 16:04:23.676][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-10-12 16:04:23.680][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-10-12 16:04:23.684][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-10-12 16:04:23.688][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:04:23.689][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:04:23.691][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:04:23.693][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:04:23.694][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:04:23.695][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-10-12 16:04:23.733][biodb::testThat]
biodb.INFO [2024-10-12 16:04:23.734][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-12 16:04:23.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:23.737][biodb::testThat]
biodb.TRACE[2024-10-12 16:04:23.741][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[2024-10-12 16:04:23.743][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:04:23.746][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-10-12 16:04:23.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:23.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:23.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:23.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:23.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:23.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:23.775][FUN] Functions in observer BiodbConfig: [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[2024-10-12 16:04:23.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:23.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:23.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:23.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:23.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.824][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:23.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:23.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:23.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:23.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:23.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:23.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:23.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:23.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:23.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:23.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:23.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:23.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:23.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:23.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:23.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:23.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.903][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:23.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:23.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.908][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:23.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:23.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:23.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:23.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.918][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:23.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:23.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:23.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:23.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:23.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:23.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:23.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:23.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:23.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:23.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:23.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:23.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:23.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:24.007][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-10-12 16:04:24.010][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:24.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:24.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:24.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:24.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:24.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.026][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:24.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:24.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.071][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.114][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.119][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.124][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.157][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.161][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.188][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.193][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.194][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.197][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.229][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.230][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.232][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.264][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.265][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.267][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.300][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.301][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.304][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.320][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.322][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.324][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.335][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.337][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.339][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.346][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.347][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.349][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.356][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.357][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.360][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.366][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.368][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.370][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.395][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[2024-10-12 16:04:24.445][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:04:24.447][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-10-12 16:04:24.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:24.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:24.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:24.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:24.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:24.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:24.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:04:24.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.512][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.522][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.533][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:24.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.610][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.615][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.626][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:24.661][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-10-12 16:04:24.690][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:24.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:24.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.695][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:24.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:24.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.700][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:24.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:24.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.709][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:24.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:24.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.727][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.770][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.775][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.781][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:24.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.826][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.827][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.830][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:24.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:24.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.847][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.852][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.857][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.863][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.864][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.867][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.868][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:24.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.899][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.903][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:24.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:24.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.923][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.928][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.933][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.938][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.939][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.942][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.943][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:24.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:24.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.973][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.974][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.976][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:24.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:24.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:24.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:24.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:24.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:25.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.008][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:25.009][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.012][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:25.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.044][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.045][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.048][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.064][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.066][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.068][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.075][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:25.076][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:25.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.079][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.085][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:25.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:25.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.089][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.095][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:25.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.104][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.110][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.111][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.114][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.120][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.121][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.124][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.130][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:25.132][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:25.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.134][ef$get] fields variable is a list.
biodb.INFO [2024-10-12 16:04:25.144][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.145][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-12 16:04:25.147][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:25.148][biodb::testThat]
biodb.DEBUG[2024-10-12 16:04:25.150][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-10-12 16:04:25.158][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-10-12 16:04:25.163][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-10-12 16:04:25.165][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-10-12 16:04:25.168][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-10-12 16:04:25.170][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-10-12 16:04:25.174][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[2024-10-12 16:04:25.175][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-10-12 16:04:25.177][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-10-12 16:04:25.178][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-10-12 16:04:25.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:25.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:25.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:25.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:25.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:25.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:04:25.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:25.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:25.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.223][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:25.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:25.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:25.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:25.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.264][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.269][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.279][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:25.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:25.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:25.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:25.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:25.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:25.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:04:25.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.343][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:25.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:25.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.348][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-12 16:04:25.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-12 16:04:25.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.354][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:25.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:25.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-12 16:04:25.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-12 16:04:25.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-12 16:04:25.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:25.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:25.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:25.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:25.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:25.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:25.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:25.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:25.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:25.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:25.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:25.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:25.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:25.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:25.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:25.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-12 16:04:25.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-12 16:04:25.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-12 16:04:25.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.433][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.438][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.448][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-10-12 16:04:25.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:25.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:25.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:25.501][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-10-12 16:04:25.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:04:25.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:04:25.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:04:25.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:04:25.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:04:25.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:04:25.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:04:25.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:04:25.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:04:25.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:04:25.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:04:25.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:04:25.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:04:25.546][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.547][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-12 16:04:25.548][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:25.549][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.557][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.558][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-12 16:04:25.559][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:25.561][biodb::testThat]
biodb.WARN [2024-10-12 16:04:25.586][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-10-12 16:04:25.612][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-10-12 16:04:25.624][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.625][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-12 16:04:25.626][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:25.627][biodb::testThat]
biodb.TRACE[2024-10-12 16:04:25.670][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:25.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:25.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:25.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:25.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:25.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:25.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:25.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:25.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.738][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:25.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:25.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:25.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:25.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.749][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:25.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:25.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:25.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:25.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:25.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:25.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:04:25.766][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.767][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-12 16:04:25.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:25.769][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.779][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.780][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-12 16:04:25.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:25.783][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.792][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.794][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-12 16:04:25.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:25.796][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.804][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.806][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-12 16:04:25.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:25.808][biodb::testThat]
biodb.INFO [2024-10-12 16:04:25.816][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:04:25.817][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-10-12 16:04:25.819][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-10-12 16:04:25.820][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:04:25.821][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:25.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:25.823][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:25.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:25.825][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.826][FUN] Functions in observer BiodbConfig: [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 [2024-10-12 16:04:25.838][biodb::testContext]
biodb.INFO [2024-10-12 16:04:25.840][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:04:25.841][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-10-12 16:04:25.842][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:04:25.843][biodb::testContext]
biodb.INFO [2024-10-12 16:04:25.846][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:04:25.852][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:04:25.857][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:25.858][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:04:25.859][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:04:25.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.864][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:04:25.865][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:04:25.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.869][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:04:25.871][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:04:25.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.875][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:04:25.876][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:04:25.878][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:04:25.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.882][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:04:25.883][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:04:25.885][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:04:25.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.889][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:04:25.890][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:04:25.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.895][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:04:25.896][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:04:25.897][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:04:25.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.902][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:04:25.903][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:04:25.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.907][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:04:25.909][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:04:25.910][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:04:25.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.914][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:04:25.916][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:04:25.917][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:04:25.918][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:04:25.920][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:04:25.922][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:04:25.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.926][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:04:25.928][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:04:25.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.932][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:04:25.934][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:04:25.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.938][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:04:25.939][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:04:25.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.944][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:04:25.945][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:04:25.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.950][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:04:25.952][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:04:25.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.956][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:04:25.957][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:04:25.968][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:04:25.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.972][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:04:25.974][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:04:25.975][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:04:25.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:25.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:25.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:25.980][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:04:25.982][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:25.983][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-12 16:04:25.984][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:25.985][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:25.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:25.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:25.989][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:25.990][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:25.991][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:04:25.993][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:25.994][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:25.995][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:04:25.996][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:25.998][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:25.999][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.000][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:26.000][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:04:26.000][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:04:26.000][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:04:26.000][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:04:26.001][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:26.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.005][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:26.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.008][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.009][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.011][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:26.012][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:26.013][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.014][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.015][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:04:26.018][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.019][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:04:26.020][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.021][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:26.023][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.027][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:04:26.029][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:26.034][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.035][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:04:26.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:26.038][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.039][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.040][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:26.040][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:04:26.040][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:04:26.040][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:04:26.040][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:04:26.042][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:26.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.045][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:26.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.049][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.050][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.051][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:26.052][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:26.054][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.055][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.056][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:04:26.059][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.060][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-12 16:04:26.061][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.063][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:26.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.065][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.066][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.068][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.069][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:04:26.070][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:26.071][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.072][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:04:26.074][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:26.075][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.077][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.079][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:26.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.082][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:26.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.086][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.087][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.088][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:26.089][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:26.090][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.091][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.093][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:04:26.095][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.096][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:04:26.097][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.099][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:26.100][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.101][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.102][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.104][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.105][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:04:26.106][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:26.107][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.109][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:04:26.110][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:26.111][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.112][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.113][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.115][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:26.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.118][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:26.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.122][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.123][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.124][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:26.125][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:26.126][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.128][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.129][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:26.130][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.232][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:04:26.234][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:04:26.235][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:04:26.237][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:04:26.239][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:04:26.240][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:04:26.242][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:04:26.244][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:04:26.246][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:04:26.247][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:04:26.249][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:04:26.251][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:04:26.252][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:04:26.254][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:04:26.256][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:04:26.258][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:04:26.260][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:04:26.261][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:04:26.263][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:04:26.265][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:04:26.267][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:04:26.268][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:04:26.270][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:04:26.272][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:04:26.274][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:04:26.275][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:04:26.277][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:04:26.279][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:04:26.280][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:04:26.282][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:04:26.284][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:04:26.285][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:04:26.287][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:04:26.289][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:04:26.290][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:04:26.292][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:04:26.294][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:04:26.296][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:04:26.297][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:04:26.299][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:04:26.301][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:04:26.302][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:04:26.304][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:04:26.306][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:04:26.307][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:04:26.309][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:04:26.311][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:04:26.313][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:04:26.314][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:04:26.316][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:04:26.318][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:04:26.319][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:04:26.321][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:04:26.323][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:04:26.324][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:04:26.326][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:04:26.328][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:04:26.329][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:04:26.331][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:04:26.333][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:04:26.335][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:04:26.336][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:04:26.338][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:04:26.340][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:04:26.341][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:04:26.343][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:04:26.345][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:04:26.346][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:04:26.348][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:04:26.350][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:04:26.352][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:04:26.353][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:04:26.355][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:04:26.357][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:04:26.358][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:04:26.360][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:04:26.362][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:04:26.363][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:04:26.365][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:04:26.371][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:04:26.373][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:04:26.375][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:04:26.376][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:04:26.378][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:04:26.380][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:04:26.381][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:26.382][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.385][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.386][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[2024-10-12 16:04:26.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.471][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[2024-10-12 16:04:26.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.478][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[2024-10-12 16:04:26.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.486][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[2024-10-12 16:04:26.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.494][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[2024-10-12 16:04:26.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:26.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:26.522][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-10-12 16:04:26.523][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-10-12 16:04:26.526][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.527][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-10-12 16:04:26.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:26.531][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.532][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-10-12 16:04:26.534][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.536][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-10-12 16:04:26.537][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:26.543][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.544][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-10-12 16:04:26.546][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:26.547][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-10-12 16:04:26.547][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-10-12 16:04:26.547][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-10-12 16:04:26.547][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-10-12 16:04:26.547][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-10-12 16:04:26.547][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-10-12 16:04:26.547][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-10-12 16:04:26.548][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:26.549][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.551][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:04:26.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.554][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:26.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:26.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:26.558][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:26.559][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-10-12 16:04:26.559][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-10-12 16:04:26.559][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-10-12 16:04:26.559][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-10-12 16:04:26.560][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:26.561][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:26.562][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:26.564][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:26.565][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-10-12 16:04:26.569][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-10-12 16:04:26.570][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-10-12 16:04:26.572][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-10-12 16:04:26.574][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-10-12 16:04:26.575][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:04:26.576][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:04:26.578][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:04:26.579][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:04:26.581][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-10-12 16:04:26.582][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-10-12 16:04:26.583][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:04:26.585][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-10-12 16:04:26.586][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-10-12 16:04:26.587][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:04:26.588][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:26.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:26.590][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:26.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:26.592][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:26.594][FUN] Functions in observer 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 
  5.835   0.336   6.165

'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 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.8.0’
* 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)