Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-22 23:55 -0400 (Sat, 22 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4763
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4494
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4521
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 11/32HostnameOS / ArchCHECK
biodbNci 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-22 09:55 -0400 (Sat, 22 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_20
git_last_commit: d666b49
git_last_commit_date: 2024-10-29 11:09:24 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.10.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.10.0.tar.gz
StartedAt: 2025-03-22 16:04:38 -0400 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 16:05:36 -0400 (Sat, 22 Mar 2025)
EllapsedTime: 58.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
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 [2025-03-22 16:05:33.765][biodb::testContext]
biodb.INFO [2025-03-22 16:05:33.767][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:05:33.768][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-22 16:05:33.769][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:05:33.770][biodb::testContext]
biodb.INFO [2025-03-22 16:05:33.775][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:05:33.777][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:05:33.783][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:05:33.784][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:05:33.785][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:05:33.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.788][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:05:33.805][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:05:33.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.808][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:05:33.809][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:05:33.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.812][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:05:33.813][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:05:33.814][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:05:33.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.817][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:05:33.818][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:05:33.819][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:05:33.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.822][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:05:33.823][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:05:33.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.826][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:05:33.827][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:05:33.828][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:05:33.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.831][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:05:33.832][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:05:33.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.835][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:05:33.836][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:05:33.837][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:05:33.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.840][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:05:33.841][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:05:33.842][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:05:33.843][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:05:33.844][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:05:33.845][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:05:33.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.848][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:05:33.849][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:05:33.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.852][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:05:33.853][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:05:33.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.856][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:05:33.857][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:05:33.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.860][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:05:33.861][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:05:33.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.864][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:05:33.865][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:05:33.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.868][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:05:33.869][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:05:33.873][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:05:33.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.876][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:05:33.877][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:05:33.878][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:05:33.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:33.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:33.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:33.883][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:05:33.912][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:33.932][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:05:33.933][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.933][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:33.934][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:05:33.936][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:33.937][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:33.938][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:05:33.939][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:33.940][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.940][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:05:33.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:33.942][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:33.943][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.944][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:05:33.944][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:05:33.944][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:05:33.944][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:05:33.944][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:05:33.945][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:05:33.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:33.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:33.947][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:33.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:33.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:33.950][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:33.951][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:33.952][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:33.952][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:33.953][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:33.954][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:33.955][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:05:33.957][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:33.958][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:05:33.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:33.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:05:33.962][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:33.963][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:33.964][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:05:33.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:33.966][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.966][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:05:33.967][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:33.968][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:33.969][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.970][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:05:33.970][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:05:33.970][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:05:33.970][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:05:33.970][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:05:33.971][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:05:33.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:33.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:33.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:33.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:33.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:33.976][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:33.977][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:33.978][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:33.978][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:33.979][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:33.980][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:33.981][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:05:33.983][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.984][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:05:33.984][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.985][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:33.986][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.987][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:05:33.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:33.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:33.990][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:05:33.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:33.991][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:33.992][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:05:33.993][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:33.994][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:33.995][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:33.996][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:33.997][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:05:33.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:33.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:33.999][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:34.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:34.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:34.002][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:34.003][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:34.003][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:34.004][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:34.005][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:34.006][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:34.007][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:05:34.008][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:34.009][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:05:34.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:34.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:34.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:34.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:05:34.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:34.015][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:34.015][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:05:34.016][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:34.017][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:34.018][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:05:34.019][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:34.020][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:34.021][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:34.022][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:34.023][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:05:34.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:34.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:34.025][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:34.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:34.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:34.027][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:34.028][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:34.029][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:34.030][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:34.031][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:34.032][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:34.035][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:05:34.036][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.085][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[2025-03-22 16:05:34.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.092][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[2025-03-22 16:05:34.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.100][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[2025-03-22 16:05:34.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.108][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[2025-03-22 16:05:34.109][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:05:34.113][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:05:34.114][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:05:34.115][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:05:34.117][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:05:34.118][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:05:34.119][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:05:34.120][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:05:34.122][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:05:34.123][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:05:34.124][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:05:34.125][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:05:34.127][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:05:34.128][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:05:34.129][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:05:34.130][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:05:34.131][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:05:34.133][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:05:34.134][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:05:34.135][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:05:34.136][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:05:34.138][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:05:34.139][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:05:34.140][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:05:34.141][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:05:34.143][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:05:34.144][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:05:34.145][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:05:34.146][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:05:34.148][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:05:34.149][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:05:34.150][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:05:34.151][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:05:34.153][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:05:34.154][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:05:34.155][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:05:34.156][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:05:34.158][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:05:34.159][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:05:34.160][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:05:34.161][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:05:34.162][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:05:34.164][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:05:34.165][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:05:34.166][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:05:34.167][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:05:34.169][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:05:34.170][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:05:34.171][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:05:34.172][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:05:34.174][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:05:34.175][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:05:34.176][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:05:34.177][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:05:34.179][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:05:34.180][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:05:34.181][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:05:34.182][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:05:34.184][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:05:34.185][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:05:34.186][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:05:34.187][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:05:34.189][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:05:34.190][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:05:34.191][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:05:34.192][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:05:34.194][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:05:34.195][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:05:34.196][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:05:34.197][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:05:34.199][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:05:34.200][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:05:34.201][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:05:34.202][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:05:34.203][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:05:34.205][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:05:34.206][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:05:34.207][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:05:34.208][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:05:34.210][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:05:34.211][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:05:34.212][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:05:34.213][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:05:34.219][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:05:34.220][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:05:34.223][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:05:34.224][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.225][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:34.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:34.356][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-22 16:05:34.366][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-22 16:05:34.368][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:34.369][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-22 16:05:34.370][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:34.371][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:34.372][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:34.373][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-22 16:05:34.374][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:34.375][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:34.376][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-22 16:05:34.377][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:34.378][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:34.379][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-22 16:05:34.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:34.381][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-22 16:05:34.381][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-22 16:05:34.381][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-22 16:05:34.381][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-22 16:05:34.381][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-22 16:05:34.381][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-22 16:05:34.381][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-22 16:05:34.382][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:34.382][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:34.383][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:05:34.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:34.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:34.386][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:34.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:34.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:34.389][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:34.390][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-22 16:05:34.390][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-22 16:05:34.390][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-22 16:05:34.390][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-22 16:05:34.391][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:34.392][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:34.393][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:34.393][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:34.399][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-22 16:05:34.420][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-22 16:05:34.421][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-22 16:05:34.425][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-22 16:05:34.429][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-22 16:05:34.433][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:05:34.434][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:05:34.435][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:05:34.436][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:05:34.438][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:05:34.439][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-22 16:05:34.447][biodb::testThat]
biodb.INFO [2025-03-22 16:05:34.448][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-22 16:05:34.449][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:34.450][biodb::testThat]
biodb.TRACE[2025-03-22 16:05:34.481][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-03-22 16:05:34.482][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:05:34.485][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-22 16:05:34.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:05:34.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.507][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.TRACE[2025-03-22 16:05:34.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:34.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:34.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.567][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:34.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:34.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:34.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:34.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:34.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:34.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.594][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.597][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.604][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:05:34.664][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-03-22 16:05:34.666][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:05:34.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:05:34.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:05:34.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:05:34.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:05:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:05:34.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.676][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:05:34.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:05:34.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.706][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.736][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.739][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.743][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:34.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.766][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.767][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.768][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:34.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:34.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:34.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:34.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:34.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:34.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.790][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:34.791][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:34.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:34.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:34.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.813][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.816][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:34.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:34.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:34.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:34.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:34.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:34.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.837][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:34.838][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:34.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:34.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:34.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.860][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.861][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.873][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.874][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.883][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:34.884][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:34.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.889][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:34.890][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:34.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.896][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:34.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.898][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.901][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.902][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:34.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.904][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.919][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-03-22 16:05:34.950][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:05:34.951][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-22 16:05:34.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:05:34.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:34.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:34.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:34.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:34.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:34.960][FUN] Functions in observer BiodbConfig: [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[2025-03-22 16:05:34.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:34.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:34.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:34.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:34.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:34.998][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:34.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.002][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.006][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.024][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.057][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.061][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.068][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:05:35.093][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-03-22 16:05:35.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.115][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.121][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:05:35.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:05:35.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:05:35.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:05:35.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.135][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.164][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.168][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.171][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.199][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.200][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.212][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.215][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.219][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.222][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.223][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.226][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.249][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.250][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.252][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.265][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.269][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.272][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.273][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.276][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.296][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.297][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.299][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.319][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.320][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.343][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.344][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.356][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.357][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.362][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.363][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.365][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.368][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.372][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.374][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.378][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.379][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.381][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.385][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.386][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.391][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.392][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.397][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.398][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.400][ef$get] fields variable is a list.
biodb.INFO [2025-03-22 16:05:35.406][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.407][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-22 16:05:35.408][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:35.409][biodb::testThat]
biodb.DEBUG[2025-03-22 16:05:35.410][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-03-22 16:05:35.417][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-03-22 16:05:35.421][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-03-22 16:05:35.422][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-03-22 16:05:35.424][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-03-22 16:05:35.425][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-03-22 16:05:35.426][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-03-22 16:05:35.427][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-22 16:05:35.428][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-03-22 16:05:35.429][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-03-22 16:05:35.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:05:35.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:35.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:35.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:35.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:35.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:05:35.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.483][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.493][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:05:35.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:05:35.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:35.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:35.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:35.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:35.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:05:35.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.535][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.539][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-22 16:05:35.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.546][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-22 16:05:35.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-22 16:05:35.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-22 16:05:35.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:05:35.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:05:35.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-22 16:05:35.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-22 16:05:35.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-22 16:05:35.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.598][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.601][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.608][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-22 16:05:35.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:05:35.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:05:35.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:05:35.647][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-03-22 16:05:35.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:05:35.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:05:35.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:05:35.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:05:35.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:05:35.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:05:35.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:05:35.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:05:35.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:05:35.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:05:35.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:05:35.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:05:35.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:05:35.677][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.678][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-22 16:05:35.679][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:35.680][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.684][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.685][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-22 16:05:35.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:35.687][biodb::testThat]
biodb.WARN [2025-03-22 16:05:35.705][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-22 16:05:35.722][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-22 16:05:35.729][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.729][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-22 16:05:35.730][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:35.731][biodb::testThat]
biodb.TRACE[2025-03-22 16:05:35.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.758][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.761][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:05:35.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:05:35.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.765][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:05:35.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:05:35.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:05:35.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.804][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:05:35.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:05:35.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:05:35.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:05:35.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:05:35.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:05:35.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:05:35.815][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.816][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-22 16:05:35.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:35.818][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.824][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.825][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-22 16:05:35.825][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:35.826][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.832][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.833][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-22 16:05:35.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:35.835][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.839][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.840][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-22 16:05:35.841][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:05:35.842][biodb::testThat]
biodb.INFO [2025-03-22 16:05:35.847][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:05:35.848][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-22 16:05:35.848][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-22 16:05:35.849][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:05:35.850][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:35.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:35.852][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:35.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:35.853][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.854][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.INFO [2025-03-22 16:05:35.865][biodb::testContext]
biodb.INFO [2025-03-22 16:05:35.866][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:05:35.867][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-22 16:05:35.868][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:05:35.869][biodb::testContext]
biodb.INFO [2025-03-22 16:05:35.871][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:05:35.872][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:05:35.875][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:05:35.876][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:05:35.877][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:05:35.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.880][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:05:35.881][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:05:35.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.885][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:05:35.885][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:05:35.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.889][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:05:35.890][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:05:35.890][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:05:35.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.894][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:05:35.895][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:05:35.896][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:05:35.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.899][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:05:35.900][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:05:35.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.903][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:05:35.904][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:05:35.905][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:05:35.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.908][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:05:35.909][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:05:35.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.912][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:05:35.913][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:05:35.914][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:05:35.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.917][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:05:35.918][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:05:35.919][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:05:35.920][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:05:35.921][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:05:35.921][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:05:35.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.925][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:05:35.926][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:05:35.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.929][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:05:35.930][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:05:35.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.933][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:05:35.934][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:05:35.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.937][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:05:35.938][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:05:35.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.941][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:05:35.942][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:05:35.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.945][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:05:35.946][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:05:35.949][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:05:35.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.953][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:05:35.953][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:05:35.954][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:05:35.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:35.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:35.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:35.958][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:05:35.959][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:35.960][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:05:35.961][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:35.962][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:35.963][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:35.964][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:05:35.965][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:35.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:35.966][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:05:35.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:35.968][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:35.969][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:05:35.970][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:35.971][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:35.972][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:35.973][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:05:35.973][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:05:35.973][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:05:35.973][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:05:35.973][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:05:35.973][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:05:35.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:35.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:35.976][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:35.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:35.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:35.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:35.979][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:35.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:35.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:35.982][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:35.983][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:35.984][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:05:35.985][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:35.990][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:05:35.991][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:35.992][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:35.992][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:35.993][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:05:35.994][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:35.995][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:35.996][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:05:35.997][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:35.998][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:35.998][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:05:35.999][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:36.000][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.001][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.002][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:05:36.002][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:05:36.002][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:05:36.002][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:05:36.002][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:05:36.003][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:05:36.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:36.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:36.005][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:36.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:36.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:36.008][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.009][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.010][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:36.010][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:36.011][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.012][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.013][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:05:36.015][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.016][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:05:36.017][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.017][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:36.018][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.019][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.020][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.021][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.022][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:05:36.023][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:36.024][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.024][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:05:36.025][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:36.026][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.027][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.028][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:05:36.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:36.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:36.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:36.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:36.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:36.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.035][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.036][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:36.036][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:36.037][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.038][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.039][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:05:36.041][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.042][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:05:36.042][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.043][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:36.044][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.045][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.046][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.047][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.048][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:05:36.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:36.050][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.050][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:05:36.051][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:36.052][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.053][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.054][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.055][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:05:36.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:36.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:36.057][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:36.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:36.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:36.060][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.061][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.062][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:36.062][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:36.063][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.064][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.065][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:05:36.066][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.138][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:05:36.139][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:05:36.140][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:05:36.141][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:05:36.143][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:05:36.144][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:05:36.145][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:05:36.146][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:05:36.148][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:05:36.149][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:05:36.150][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:05:36.151][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:05:36.153][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:05:36.154][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:05:36.155][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:05:36.156][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:05:36.158][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:05:36.159][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:05:36.160][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:05:36.161][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:05:36.163][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:05:36.164][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:05:36.165][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:05:36.166][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:05:36.167][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:05:36.169][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:05:36.170][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:05:36.171][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:05:36.172][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:05:36.174][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:05:36.175][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:05:36.176][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:05:36.177][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:05:36.179][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:05:36.180][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:05:36.181][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:05:36.182][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:05:36.184][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:05:36.185][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:05:36.186][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:05:36.187][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:05:36.188][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:05:36.190][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:05:36.191][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:05:36.192][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:05:36.193][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:05:36.195][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:05:36.196][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:05:36.197][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:05:36.198][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:05:36.200][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:05:36.201][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:05:36.202][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:05:36.203][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:05:36.205][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:05:36.206][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:05:36.207][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:05:36.208][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:05:36.209][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:05:36.211][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:05:36.212][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:05:36.213][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:05:36.214][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:05:36.216][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:05:36.217][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:05:36.218][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:05:36.219][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:05:36.221][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:05:36.222][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:05:36.223][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:05:36.224][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:05:36.229][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:05:36.230][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:05:36.231][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:05:36.233][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:05:36.234][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:05:36.235][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:05:36.236][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:05:36.238][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:05:36.239][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:05:36.240][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:05:36.241][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:05:36.242][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:05:36.244][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:05:36.245][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:05:36.246][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:05:36.247][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.248][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.260][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.DEBUG[2025-03-22 16:05:36.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:05:36.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:05:36.347][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-22 16:05:36.348][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-22 16:05:36.350][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.351][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-22 16:05:36.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:05:36.354][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.354][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-22 16:05:36.355][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.356][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.357][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-22 16:05:36.358][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:05:36.359][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.360][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-22 16:05:36.361][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:05:36.362][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-22 16:05:36.362][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-22 16:05:36.362][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-22 16:05:36.362][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-22 16:05:36.362][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-22 16:05:36.362][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-22 16:05:36.362][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-22 16:05:36.363][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:05:36.363][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.364][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:05:36.365][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:36.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:36.367][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:05:36.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:05:36.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:05:36.369][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:05:36.370][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-22 16:05:36.370][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-22 16:05:36.370][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-22 16:05:36.370][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-22 16:05:36.371][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:05:36.372][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:05:36.373][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:05:36.374][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:05:36.375][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-22 16:05:36.377][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-22 16:05:36.378][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-22 16:05:36.379][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-22 16:05:36.381][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-22 16:05:36.382][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:05:36.383][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:05:36.384][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:05:36.385][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:05:36.386][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-22 16:05:36.387][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-22 16:05:36.388][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:05:36.389][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-22 16:05:36.390][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-22 16:05:36.390][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:05:36.391][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:05:36.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:05:36.393][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:05:36.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:05:36.394][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:05:36.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  3.995   0.189   4.175

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)