Back to Long Tests report for BioC 3.17

This page was generated on 2023-10-14 21:30:02 -0400 (Sat, 14 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 13/31HostnameOS / ArchCHECK
biodbNci 1.4.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-10-14 09:55:02 -0400 (Sat, 14 Oct 2023)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_17
git_last_commit: 96da121
git_last_commit_date: 2023-04-25 11:36:41 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.6.4 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1


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

raw results

Summary

Package: biodbNci
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2023-10-14 11:03:39 -0400 (Sat, 14 Oct 2023)
EndedAt: 2023-10-14 11:33:39 -0400 (Sat, 14 Oct 2023)
EllapsedTime: 1799.8 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2023-10-14 11:04:53.735][biodb::testContext]
biodb.INFO [2023-10-14 11:04:53.739][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:04:53.741][biodb::testContext] Test context - Generic long tests
biodb.INFO [2023-10-14 11:04:53.742][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:04:53.743][biodb::testContext]
biodb.INFO [2023-10-14 11:04:53.752][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:04:53.754][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:04:53.763][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:04:53.765][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:04:53.767][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:04:53.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.772][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:04:53.802][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:04:53.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.808][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:04:53.809][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:04:53.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.815][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:04:53.816][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:04:53.818][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:04:53.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.823][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:04:53.825][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:04:53.826][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:04:53.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.841][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:04:53.842][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:04:53.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.846][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:04:53.848][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:04:53.849][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:04:53.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.853][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:04:53.854][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:04:53.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.858][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:04:53.860][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:04:53.861][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:04:53.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.865][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:04:53.867][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:04:53.868][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:04:53.869][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:04:53.870][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:04:53.871][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:04:53.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.874][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[2023-10-14 11:04:53.875][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:04:53.877][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:04:53.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.881][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:04:53.882][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:04:53.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.886][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:04:53.887][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:04:53.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.891][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:04:53.893][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:04:53.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.897][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:04:53.898][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:04:53.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.902][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:04:53.904][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:04:53.915][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:04:53.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.920][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:04:53.921][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:04:53.922][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:04:53.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:53.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:53.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:53.930][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:04:53.971][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:53.991][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-10-14 11:04:53.992][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:53.993][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:04:53.995][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:53.996][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:04:53.997][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:53.998][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:04:53.999][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:04:54.000][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:04:54.002][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.003][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:04:54.004][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:04:54.005][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.006][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.007][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:04:54.007][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:04:54.007][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:04:54.007][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:04:54.007][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:04:54.009][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:04:54.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:04:54.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.017][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.018][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:04:54.019][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:04:54.020][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.021][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.022][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:04:54.025][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.026][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:04:54.027][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.028][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:04:54.029][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.030][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.032][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.034][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:04:54.035][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:04:54.036][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.037][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:04:54.039][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:04:54.040][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.041][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.042][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:04:54.042][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:04:54.042][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:04:54.042][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:04:54.042][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:04:54.043][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:04:54.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.047][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:04:54.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.050][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.051][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:04:54.053][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:04:54.054][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.056][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.057][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:04:54.059][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.060][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-10-14 11:04:54.061][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.062][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:04:54.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.065][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.066][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.067][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.068][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:04:54.070][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:04:54.071][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.072][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:04:54.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:04:54.074][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.077][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.079][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:04:54.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:04:54.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.092][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:04:54.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:04:54.096][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.097][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.098][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:04:54.100][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.102][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:04:54.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:04:54.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.108][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.109][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.110][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:04:54.111][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:04:54.112][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.114][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:04:54.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:04:54.116][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.117][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.118][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.120][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:04:54.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:04:54.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.126][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.128][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:04:54.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:04:54.131][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.132][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.137][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:04:54.138][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.155][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[2023-10-14 11:04:54.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.160][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[2023-10-14 11:04:54.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.166][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[2023-10-14 11:04:54.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.171][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[2023-10-14 11:04:54.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.182][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[2023-10-14 11:04:54.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.214][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[2023-10-14 11:04:54.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.231][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:04:54.237][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:04:54.238][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:04:54.240][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:04:54.242][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:04:54.244][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:04:54.246][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:04:54.247][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:04:54.249][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:04:54.251][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:04:54.252][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:04:54.254][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:04:54.256][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:04:54.257][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:04:54.259][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:04:54.261][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:04:54.263][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:04:54.264][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:04:54.266][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:04:54.268][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:04:54.269][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:04:54.271][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:04:54.273][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:04:54.275][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:04:54.276][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:04:54.278][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:04:54.280][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:04:54.282][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:04:54.283][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:04:54.285][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:04:54.287][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:04:54.288][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:04:54.290][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:04:54.292][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:04:54.294][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:04:54.295][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:04:54.297][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:04:54.299][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:04:54.300][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:04:54.302][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:04:54.304][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:04:54.305][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:04:54.307][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:04:54.309][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:04:54.311][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:04:54.312][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:04:54.314][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:04:54.316][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:04:54.317][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:04:54.319][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:04:54.321][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:04:54.323][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:04:54.325][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:04:54.332][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:04:54.334][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:04:54.336][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:04:54.337][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:04:54.339][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:04:54.341][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:04:54.342][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:04:54.344][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:04:54.346][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:04:54.348][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:04:54.350][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:04:54.352][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:04:54.353][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:04:54.355][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:04:54.357][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:04:54.359][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:04:54.361][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:04:54.363][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:04:54.365][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:04:54.366][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:04:54.368][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:04:54.370][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:04:54.372][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:04:54.374][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:04:54.376][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:04:54.378][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:04:54.380][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:04:54.382][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:04:54.384][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:04:54.386][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:04:54.393][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:04:54.396][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:04:54.400][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:04:54.401][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.403][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.424][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[2023-10-14 11:04:54.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.439][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[2023-10-14 11:04:54.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.454][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[2023-10-14 11:04:54.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:04:54.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:04:54.538][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2023-10-14 11:04:54.549][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2023-10-14 11:04:54.551][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.553][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2023-10-14 11:04:54.554][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.555][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:04:54.556][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.557][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-10-14 11:04:54.558][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.561][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2023-10-14 11:04:54.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:04:54.563][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.565][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2023-10-14 11:04:54.570][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:04:54.571][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2023-10-14 11:04:54.571][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2023-10-14 11:04:54.571][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2023-10-14 11:04:54.571][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2023-10-14 11:04:54.571][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2023-10-14 11:04:54.571][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2023-10-14 11:04:54.571][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2023-10-14 11:04:54.573][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:04:54.574][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.575][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:04:54.576][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:04:54.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:04:54.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:04:54.582][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:04:54.583][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2023-10-14 11:04:54.583][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2023-10-14 11:04:54.583][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2023-10-14 11:04:54.583][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2023-10-14 11:04:54.584][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:04:54.585][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:04:54.586][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:04:54.587][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:04:54.594][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2023-10-14 11:04:54.619][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2023-10-14 11:04:54.620][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2023-10-14 11:04:54.625][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2023-10-14 11:04:54.630][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2023-10-14 11:04:54.635][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:04:54.636][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:04:54.637][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-10-14 11:04:54.639][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-10-14 11:04:54.640][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-10-14 11:04:54.641][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2023-10-14 11:04:54.653][biodb::testThat]
biodb.INFO [2023-10-14 11:04:54.654][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-10-14 11:04:54.655][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:04:54.656][biodb::testThat]
biodb.TRACE[2023-10-14 11:04:54.660][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2023-10-14 11:04:54.662][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:04:54.666][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2023-10-14 11:04:54.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:04:54.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:54.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:54.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:54.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:54.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:54.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-10-14 11:04:54.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.746][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:54.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:54.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:54.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:54.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:54.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:54.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:54.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:54.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.799][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:54.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:54.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:54.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:54.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:54.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:54.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.813][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.819][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:54.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:54.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.832][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:54.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:54.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.841][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:54.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:54.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:04:54.913][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2023-10-14 11:04:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:04:54.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:04:54.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.920][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:04:54.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:04:54.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.925][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:04:54.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:04:54.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.930][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:04:54.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:04:54.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.972][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:54.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:54.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:54.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:54.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:54.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.043][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.047][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.052][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.079][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.080][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.081][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.082][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.112][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.114][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.115][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.116][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.145][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.147][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.148][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.149][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.179][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.180][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.182][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.183][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.219][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.221][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.224][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.225][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.247][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.248][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.249][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.250][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.257][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.258][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.260][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.267][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.268][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.271][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.277][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.279][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.281][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.287][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.289][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.290][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.291][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.313][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2023-10-14 11:04:55.357][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2023-10-14 11:04:55.358][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2023-10-14 11:04:55.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:04:55.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:04:55.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:04:55.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:04:55.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:04:55.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:04:55.372][FUN] Functions in observer BiodbConfig: [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[2023-10-14 11:04:55.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.422][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.427][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.432][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.436][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.504][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.518][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:04:55.549][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2023-10-14 11:04:55.574][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:04:55.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:04:55.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:04:55.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:04:55.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.584][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:04:55.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:04:55.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.588][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:04:55.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:04:55.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.608][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.648][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.654][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.659][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:04:55.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.703][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.704][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.705][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.706][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.723][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.728][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.733][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.738][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.739][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.740][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.741][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.742][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.772][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.774][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.775][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.776][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.802][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.811][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.815][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:55.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:55.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.873][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.874][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.875][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.876][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:55.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.918][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.930][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.932][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.934][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:55.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:55.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.964][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.965][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.967][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.968][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:55.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.984][ef$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:04:55.985][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:04:55.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.988][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:55.994][ef$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.995][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:04:55.997][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:55.998][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:56.004][ef$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:04:56.006][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:04:56.007][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:56.008][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:56.014][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:04:56.016][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:04:56.017][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:56.018][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:56.024][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:04:56.026][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:04:56.027][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:56.032][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:56.039][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:56.040][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:04:56.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:56.042][ef$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:04:56.049][ef$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:04:56.050][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:04:56.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:04:56.052][ef$get] fields variable is a list.
biodb.INFO [2023-10-14 11:04:56.063][biodb::testThat]
biodb.INFO [2023-10-14 11:04:56.064][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-10-14 11:04:56.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:04:56.067][biodb::testThat]
biodb.DEBUG[2023-10-14 11:04:56.069][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2023-10-14 11:04:56.077][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2023-10-14 11:04:56.081][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2023-10-14 11:04:56.082][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2023-10-14 11:04:56.083][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2023-10-14 11:04:56.084][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2023-10-14 11:04:56.086][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2023-10-14 11:05:02.690][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactus14f5672112e44gz".
biodb.TRACE[2023-10-14 11:05:02.691][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2023-10-14 11:05:02.692][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2023-10-14 11:05:02.694][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2023-10-14 11:05:02.695][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2023-10-14 11:05:02.698][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker14f5645f4acddmarker".
biodb.TRACE[2023-10-14 11:05:02.699][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2023-10-14 11:05:02.700][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-10-14 11:05:02.702][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2023-10-14 11:05:02.704][self$download] Extract whole database of nci.cactus.
biodb.INFO [2023-10-14 11:05:02.705][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2023-10-14 11:05:02.707][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2023-10-14 11:06:18.874][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2023-10-14 11:06:18.876][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2023-10-14 11:32:00.691][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2023-10-14 11:32:01.162][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2023-10-14 11:33:36.143][self$addFilesToCache] Done adding files.
biodb.DEBUG[2023-10-14 11:33:36.150][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2023-10-14 11:33:36.212][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker14f564281050cmarker".
biodb.TRACE[2023-10-14 11:33:36.215][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2023-10-14 11:33:36.217][self$addFilesToCache] Done adding files.
biodb.TRACE[2023-10-14 11:33:36.220][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2023-10-14 11:33:36.223][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-10-14 11:33:36.226][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2023-10-14 11:33:36.229][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2023-10-14 11:33:36.232][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2023-10-14 11:33:36.234][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2023-10-14 11:33:36.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:33:36.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:36.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:36.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:36.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:36.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:36.260][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.TRACE[2023-10-14 11:33:36.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.293][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:33:36.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:33:36.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:33:36.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:33:36.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:33:36.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:33:36.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:33:36.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:33:36.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:33:36.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:33:36.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:33:36.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:33:36.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:33:36.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:33:36.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:33:36.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:33:36.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.345][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.351][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.364][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:33:36.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-10-14 11:33:36.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:36.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:36.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:36.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:36.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:36.404][FUN] Functions in observer BiodbConfig: [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[2023-10-14 11:33:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.437][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:33:36.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:33:36.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.443][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2023-10-14 11:33:36.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2023-10-14 11:33:36.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:33:36.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:33:36.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-10-14 11:33:36.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-10-14 11:33:36.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:33:36.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:33:36.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-10-14 11:33:36.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-10-14 11:33:36.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:33:36.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:33:36.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.481][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:33:36.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:33:36.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:33:36.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:33:36.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:33:36.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:33:36.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:33:36.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:33:36.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:33:36.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:33:36.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-10-14 11:33:36.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-10-14 11:33:36.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:33:36.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:33:36.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-10-14 11:33:36.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-10-14 11:33:36.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:33:36.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:33:36.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-10-14 11:33:36.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-10-14 11:33:36.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.543][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.548][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.560][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2023-10-14 11:33:36.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-10-14 11:33:36.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-10-14 11:33:36.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-10-14 11:33:36.619][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2023-10-14 11:33:36.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-14 11:33:36.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-14 11:33:36.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:33:36.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:33:36.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:33:36.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:33:36.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-10-14 11:33:36.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-10-14 11:33:36.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:33:36.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-10-14 11:33:36.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:33:36.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-10-14 11:33:36.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-14 11:33:36.677][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.679][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-10-14 11:33:36.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:33:36.682][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.693][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.694][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-10-14 11:33:36.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:33:36.697][biodb::testThat]
biodb.WARN [2023-10-14 11:33:36.743][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2023-10-14 11:33:36.778][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2023-10-14 11:33:36.795][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.797][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-10-14 11:33:36.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:33:36.800][biodb::testThat]
biodb.TRACE[2023-10-14 11:33:36.844][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:33:36.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:33:36.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.850][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:33:36.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:33:36.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.856][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:33:36.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:33:36.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:33:36.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:33:36.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.920][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:33:36.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:33:36.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.926][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-10-14 11:33:36.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-10-14 11:33:36.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.932][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-10-14 11:33:36.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-10-14 11:33:36.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-10-14 11:33:36.938][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-10-14 11:33:36.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-10-14 11:33:36.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-10-14 11:33:36.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-10-14 11:33:36.955][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.956][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-10-14 11:33:36.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:33:36.959][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.972][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.973][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-10-14 11:33:36.975][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:33:36.976][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.989][biodb::testThat]
biodb.INFO [2023-10-14 11:33:36.990][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-10-14 11:33:36.992][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:33:36.993][biodb::testThat]
biodb.INFO [2023-10-14 11:33:37.004][biodb::testThat]
biodb.INFO [2023-10-14 11:33:37.006][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-10-14 11:33:37.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-10-14 11:33:37.009][biodb::testThat]
biodb.INFO [2023-10-14 11:33:37.019][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:33:37.021][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2023-10-14 11:33:37.023][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2023-10-14 11:33:37.024][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:33:37.026][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.028][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.031][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-10-14 11:33:37.050][biodb::testContext]
biodb.INFO [2023-10-14 11:33:37.052][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:33:37.053][biodb::testContext] Test context - Example long tests
biodb.INFO [2023-10-14 11:33:37.055][biodb::testContext] ********************************************************************************
biodb.INFO [2023-10-14 11:33:37.056][biodb::testContext]
biodb.INFO [2023-10-14 11:33:37.061][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:33:37.065][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2023-10-14 11:33:37.071][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:33:37.073][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-10-14 11:33:37.074][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-10-14 11:33:37.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.079][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-10-14 11:33:37.081][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-10-14 11:33:37.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.086][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-10-14 11:33:37.088][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-10-14 11:33:37.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.093][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-10-14 11:33:37.095][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-10-14 11:33:37.096][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-10-14 11:33:37.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.102][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-10-14 11:33:37.103][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-10-14 11:33:37.104][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-10-14 11:33:37.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.110][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-10-14 11:33:37.111][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-10-14 11:33:37.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.117][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-10-14 11:33:37.118][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-10-14 11:33:37.120][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-10-14 11:33:37.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.125][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-10-14 11:33:37.127][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-10-14 11:33:37.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.132][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-10-14 11:33:37.133][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-10-14 11:33:37.135][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-10-14 11:33:37.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.140][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:33:37.142][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-10-14 11:33:37.143][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-10-14 11:33:37.145][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-10-14 11:33:37.146][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-10-14 11:33:37.148][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-10-14 11:33:37.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.153][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-10-14 11:33:37.154][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-10-14 11:33:37.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.160][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-10-14 11:33:37.161][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-10-14 11:33:37.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.167][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-10-14 11:33:37.168][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-10-14 11:33:37.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.173][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-10-14 11:33:37.175][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-10-14 11:33:37.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.180][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-10-14 11:33:37.182][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-10-14 11:33:37.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.187][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-10-14 11:33:37.189][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-10-14 11:33:37.205][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-10-14 11:33:37.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.211][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-10-14 11:33:37.212][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-10-14 11:33:37.214][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-10-14 11:33:37.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.220][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-10-14 11:33:37.223][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.225][self$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[2023-10-14 11:33:37.226][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.228][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:33:37.229][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.231][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.232][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.234][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.235][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:33:37.237][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:33:37.238][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.240][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-10-14 11:33:37.241][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:33:37.243][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.244][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.246][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:33:37.246][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:33:37.246][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:33:37.246][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:33:37.246][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:33:37.247][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:33:37.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.252][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:33:37.253][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.254][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.256][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.257][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.259][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:33:37.260][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:33:37.262][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.263][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.265][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-10-14 11:33:37.268][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.269][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:33:37.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.272][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:33:37.274][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.275][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.277][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.278][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.280][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:33:37.281][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:33:37.283][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.284][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-10-14 11:33:37.286][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:33:37.287][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.289][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.290][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-10-14 11:33:37.290][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-10-14 11:33:37.290][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-10-14 11:33:37.290][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-10-14 11:33:37.290][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-10-14 11:33:37.292][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:33:37.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.295][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.296][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:33:37.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.302][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.304][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:33:37.305][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:33:37.306][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.308][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.310][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-10-14 11:33:37.312][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.314][self$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[2023-10-14 11:33:37.316][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.317][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:33:37.319][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.320][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.322][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.323][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.325][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-10-14 11:33:37.326][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:33:37.328][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.329][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-10-14 11:33:37.331][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:33:37.332][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.334][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.335][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:33:37.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.341][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:33:37.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.346][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.347][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.349][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:33:37.350][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:33:37.351][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.353][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.355][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-10-14 11:33:37.357][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.359][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-10-14 11:33:37.360][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.362][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:33:37.363][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.364][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.366][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.369][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-10-14 11:33:37.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:33:37.372][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.373][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-10-14 11:33:37.375][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:33:37.376][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.378][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.379][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.380][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-10-14 11:33:37.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:33:37.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.389][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.390][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:33:37.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:33:37.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.396][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.398][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:33:37.399][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.401][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[2023-10-14 11:33:37.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.447][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[2023-10-14 11:33:37.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.480][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[2023-10-14 11:33:37.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.515][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-10-14 11:33:37.517][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-10-14 11:33:37.519][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-10-14 11:33:37.522][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-10-14 11:33:37.524][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-10-14 11:33:37.526][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-10-14 11:33:37.528][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-10-14 11:33:37.530][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-10-14 11:33:37.532][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-10-14 11:33:37.534][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-10-14 11:33:37.537][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-10-14 11:33:37.539][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-10-14 11:33:37.541][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-10-14 11:33:37.543][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-10-14 11:33:37.545][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-10-14 11:33:37.547][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-10-14 11:33:37.550][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-10-14 11:33:37.552][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-10-14 11:33:37.554][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-10-14 11:33:37.556][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-10-14 11:33:37.558][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-10-14 11:33:37.560][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-10-14 11:33:37.562][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-10-14 11:33:37.564][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-10-14 11:33:37.567][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-10-14 11:33:37.569][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-10-14 11:33:37.571][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-10-14 11:33:37.573][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-10-14 11:33:37.575][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-10-14 11:33:37.577][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-10-14 11:33:37.579][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-10-14 11:33:37.581][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-10-14 11:33:37.583][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-10-14 11:33:37.586][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-10-14 11:33:37.588][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-10-14 11:33:37.590][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-10-14 11:33:37.592][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-10-14 11:33:37.594][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-10-14 11:33:37.596][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-10-14 11:33:37.599][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-10-14 11:33:37.601][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-10-14 11:33:37.603][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-10-14 11:33:37.605][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-10-14 11:33:37.607][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-10-14 11:33:37.609][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-10-14 11:33:37.611][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-10-14 11:33:37.613][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-10-14 11:33:37.616][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-10-14 11:33:37.618][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-10-14 11:33:37.620][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-10-14 11:33:37.622][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-10-14 11:33:37.624][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-10-14 11:33:37.626][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-10-14 11:33:37.628][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-10-14 11:33:37.630][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-10-14 11:33:37.632][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-10-14 11:33:37.634][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-10-14 11:33:37.636][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-10-14 11:33:37.638][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-10-14 11:33:37.640][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-10-14 11:33:37.642][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-10-14 11:33:37.644][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-10-14 11:33:37.646][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-10-14 11:33:37.648][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-10-14 11:33:37.650][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-10-14 11:33:37.652][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-10-14 11:33:37.654][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-10-14 11:33:37.656][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-10-14 11:33:37.659][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-10-14 11:33:37.661][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-10-14 11:33:37.663][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-10-14 11:33:37.665][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-10-14 11:33:37.667][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-10-14 11:33:37.669][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-10-14 11:33:37.671][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-10-14 11:33:37.673][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-10-14 11:33:37.675][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-10-14 11:33:37.677][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-10-14 11:33:37.679][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-10-14 11:33:37.681][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-10-14 11:33:37.683][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-10-14 11:33:37.685][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-10-14 11:33:37.687][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-10-14 11:33:37.689][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-10-14 11:33:37.691][initialize] This is biodb version 1.8.1.
biodb.DEBUG[2023-10-14 11:33:37.693][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-10-14 11:33:37.694][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.697][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.826][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.DEBUG[2023-10-14 11:33:37.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-10-14 11:33:37.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-10-14 11:33:37.859][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2023-10-14 11:33:37.865][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2023-10-14 11:33:37.869][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.871][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2023-10-14 11:33:37.872][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-10-14 11:33:37.876][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.878][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2023-10-14 11:33:37.880][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.881][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.883][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2023-10-14 11:33:37.885][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-10-14 11:33:37.887][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.889][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2023-10-14 11:33:37.891][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-10-14 11:33:37.892][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2023-10-14 11:33:37.892][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2023-10-14 11:33:37.892][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2023-10-14 11:33:37.892][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2023-10-14 11:33:37.892][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2023-10-14 11:33:37.892][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2023-10-14 11:33:37.892][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2023-10-14 11:33:37.894][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-10-14 11:33:37.896][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.897][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-10-14 11:33:37.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.901][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-10-14 11:33:37.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-10-14 11:33:37.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-10-14 11:33:37.905][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-10-14 11:33:37.907][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2023-10-14 11:33:37.907][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2023-10-14 11:33:37.907][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2023-10-14 11:33:37.907][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2023-10-14 11:33:37.908][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-10-14 11:33:37.909][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-10-14 11:33:37.911][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-10-14 11:33:37.912][self$setPropertyValue]
biodb.DEBUG[2023-10-14 11:33:37.914][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2023-10-14 11:33:37.920][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2023-10-14 11:33:37.921][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2023-10-14 11:33:37.923][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2023-10-14 11:33:37.926][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2023-10-14 11:33:37.928][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:33:37.929][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-10-14 11:33:37.931][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-10-14 11:33:37.933][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-10-14 11:33:37.934][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2023-10-14 11:33:37.936][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2023-10-14 11:33:37.937][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-10-14 11:33:37.939][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2023-10-14 11:33:37.940][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2023-10-14 11:33:37.942][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-10-14 11:33:37.943][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-10-14 11:33:37.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-10-14 11:33:37.946][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-10-14 11:33:37.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-10-14 11:33:37.948][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-10-14 11:33:37.950][FUN] Functions in observer 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 
1242.828  249.174 1726.434

'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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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 ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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 -single_module -multiply_defined suppress -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-3.17-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)