Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-29 23:55 -0400 (Sat, 29 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
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: 2025-03-29 09:55 -0400 (Sat, 29 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  OK  
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: 2025-03-29 16:04:57 -0400 (Sat, 29 Mar 2025)
EndedAt: 2025-03-29 16:05:56 -0400 (Sat, 29 Mar 2025)
EllapsedTime: 59.0 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 [2025-03-29 16:05:53.004][biodb::testContext]
biodb.INFO [2025-03-29 16:05:53.005][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:05:53.006][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-29 16:05:53.007][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:05:53.008][biodb::testContext]
biodb.INFO [2025-03-29 16:05:53.013][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:05:53.015][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:05:53.021][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:05:53.022][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:05:53.023][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:05:53.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.027][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:05:53.043][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:05:53.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.045][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[2025-03-29 16:05:53.046][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:05:53.047][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:05:53.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.050][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:05:53.051][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:05:53.052][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:05:53.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.055][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:05:53.056][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:05:53.057][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:05:53.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.060][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:05:53.061][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:05:53.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.064][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:05:53.065][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:05:53.066][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:05:53.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.069][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:05:53.070][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:05:53.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.073][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[2025-03-29 16:05:53.073][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:05:53.074][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:05:53.075][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:05:53.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.078][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:05:53.079][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:05:53.080][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:05:53.081][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:05:53.082][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:05:53.083][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:05:53.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.085][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[2025-03-29 16:05:53.086][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:05:53.087][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:05:53.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.090][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:05:53.091][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:05:53.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.094][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:05:53.095][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:05:53.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.099][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:05:53.099][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:05:53.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.102][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[2025-03-29 16:05:53.103][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:05:53.104][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:05:53.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.107][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:05:53.108][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:05:53.111][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:05:53.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.113][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[2025-03-29 16:05:53.114][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:05:53.115][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:05:53.116][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:05:53.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.122][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:05:53.151][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.171][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-29 16:05:53.172][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.173][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:53.173][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.174][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.175][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.176][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.177][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:05:53.178][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:53.179][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.179][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:05:53.180][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:53.181][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.182][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.183][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:05:53.183][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:05:53.183][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:05:53.183][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:05:53.183][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:05:53.184][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:05:53.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:53.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.189][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.190][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.191][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:53.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:53.192][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.193][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.194][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:05:53.196][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.197][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:05:53.198][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.198][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:53.199][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.201][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.203][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:05:53.204][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:53.205][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.206][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:05:53.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:53.208][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.208][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.209][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:05:53.209][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:05:53.209][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:05:53.209][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:05:53.209][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:05:53.210][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:05:53.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.213][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:53.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.216][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.217][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:53.218][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:53.219][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.219][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.220][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:05:53.222][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.223][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-29 16:05:53.224][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:53.226][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.226][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.227][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.228][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.229][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:05:53.230][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:53.231][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.232][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:05:53.233][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:53.233][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.234][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.235][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.236][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:05:53.237][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.239][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:53.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.240][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.241][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.242][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.243][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:53.244][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:53.244][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.245][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.246][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:05:53.248][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.249][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:05:53.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.250][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:53.251][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.252][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.253][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.254][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.255][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:05:53.256][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:53.257][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.257][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:05:53.258][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:53.259][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.260][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.261][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.262][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:05:53.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.264][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:53.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.267][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.268][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:53.269][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:53.270][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.271][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.274][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:05:53.275][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.276][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[2025-03-29 16:05:53.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.288][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[2025-03-29 16:05:53.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.304][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[2025-03-29 16:05:53.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.307][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[2025-03-29 16:05:53.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.315][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[2025-03-29 16:05:53.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.319][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[2025-03-29 16:05:53.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.331][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[2025-03-29 16:05:53.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.346][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[2025-03-29 16:05:53.347][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:05:53.351][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:05:53.352][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:05:53.354][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:05:53.355][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:05:53.356][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:05:53.357][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:05:53.359][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:05:53.360][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:05:53.361][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:05:53.362][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:05:53.363][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:05:53.365][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:05:53.366][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:05:53.367][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:05:53.368][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:05:53.370][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:05:53.371][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:05:53.372][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:05:53.373][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:05:53.375][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:05:53.376][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:05:53.377][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:05:53.378][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:05:53.380][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:05:53.381][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:05:53.382][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:05:53.383][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:05:53.385][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:05:53.386][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:05:53.387][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:05:53.388][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:05:53.389][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:05:53.391][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:05:53.392][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:05:53.393][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:05:53.394][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:05:53.396][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:05:53.397][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:05:53.398][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:05:53.399][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:05:53.400][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:05:53.402][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:05:53.403][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:05:53.404][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:05:53.405][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:05:53.407][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:05:53.408][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:05:53.409][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:05:53.410][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:05:53.412][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:05:53.413][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:05:53.414][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:05:53.415][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:05:53.417][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:05:53.418][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:05:53.419][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:05:53.420][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:05:53.421][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:05:53.423][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:05:53.424][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:05:53.425][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:05:53.426][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:05:53.428][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:05:53.429][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:05:53.430][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:05:53.431][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:05:53.433][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:05:53.434][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:05:53.435][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:05:53.436][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:05:53.437][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:05:53.439][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:05:53.440][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:05:53.441][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:05:53.442][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:05:53.444][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:05:53.445][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:05:53.446][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:05:53.447][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:05:53.449][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:05:53.450][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:05:53.451][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:05:53.456][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:05:53.458][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:05:53.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:05:53.461][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.469][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:53.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:53.596][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-29 16:05:53.605][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-29 16:05:53.607][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.608][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-29 16:05:53.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:53.611][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.612][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-29 16:05:53.613][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.615][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-29 16:05:53.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:53.617][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.618][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-29 16:05:53.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:53.620][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-29 16:05:53.620][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-29 16:05:53.620][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-29 16:05:53.620][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-29 16:05:53.620][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-29 16:05:53.620][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-29 16:05:53.620][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-29 16:05:53.621][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:53.622][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.623][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:05:53.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:53.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:53.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:53.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:53.629][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-29 16:05:53.629][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-29 16:05:53.629][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-29 16:05:53.629][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-29 16:05:53.630][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:53.631][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:53.632][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:53.633][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:53.638][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-29 16:05:53.660][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-29 16:05:53.661][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-29 16:05:53.665][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-29 16:05:53.669][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-29 16:05:53.672][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:05:53.673][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:05:53.674][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:05:53.676][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:05:53.677][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:05:53.678][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-29 16:05:53.686][biodb::testThat]
biodb.INFO [2025-03-29 16:05:53.687][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-29 16:05:53.687][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:53.688][biodb::testThat]
biodb.TRACE[2025-03-29 16:05:53.722][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[2025-03-29 16:05:53.723][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:05:53.726][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-29 16:05:53.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:05:53.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:53.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:53.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:53.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:53.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:53.748][FUN] Functions in observer BiodbConfig: [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[2025-03-29 16:05:53.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:53.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:53.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:53.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:53.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:53.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:53.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:53.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:53.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:53.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:53.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:53.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:53.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:53.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:53.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:53.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:53.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.835][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.838][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.846][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:05:53.906][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-03-29 16:05:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:05:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:05:53.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.911][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:05:53.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:05:53.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.915][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:05:53.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:05:53.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.919][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:05:53.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:05:53.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.949][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:53.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.979][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.982][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.986][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:53.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:53.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:53.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:53.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.009][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.010][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.012][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.030][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.033][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.034][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.037][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.057][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.058][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.080][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.081][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.104][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.105][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.107][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.117][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.118][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.127][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.128][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.134][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.134][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.140][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.141][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.142][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.146][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.147][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.164][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[2025-03-29 16:05:54.196][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:05:54.197][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-29 16:05:54.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:05:54.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:54.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:54.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:54.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:54.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:54.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:05:54.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.241][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.245][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.249][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.305][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.308][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.315][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:05:54.340][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-03-29 16:05:54.359][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:05:54.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:05:54.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.363][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:05:54.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:05:54.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.370][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:05:54.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:05:54.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.373][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:05:54.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:05:54.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.384][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.417][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.421][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.449][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.450][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.452][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.463][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.466][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.470][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.473][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.474][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.476][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.477][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.501][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.502][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.503][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.514][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.517][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.524][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.525][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.548][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.549][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.572][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.573][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.596][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.597][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.609][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.610][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.612][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.615][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.616][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.621][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.626][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.628][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.631][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.632][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.637][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.638][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.640][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.644][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.645][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.646][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.650][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.651][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.653][ef$get] fields variable is a list.
biodb.INFO [2025-03-29 16:05:54.658][biodb::testThat]
biodb.INFO [2025-03-29 16:05:54.659][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-29 16:05:54.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:54.661][biodb::testThat]
biodb.DEBUG[2025-03-29 16:05:54.663][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-03-29 16:05:54.669][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-03-29 16:05:54.673][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-03-29 16:05:54.675][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-03-29 16:05:54.676][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-03-29 16:05:54.677][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-03-29 16:05:54.679][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[2025-03-29 16:05:54.680][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-29 16:05:54.681][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-03-29 16:05:54.682][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-03-29 16:05:54.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:05:54.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:54.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:54.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:54.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:54.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:54.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:05:54.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.736][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.739][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.746][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:05:54.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:05:54.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:54.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:54.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:54.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:54.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:54.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:05:54.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.788][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.792][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:05:54.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.796][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:05:54.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:05:54.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:05:54.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:05:54.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:05:54.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:05:54.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:05:54.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:05:54.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.851][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.855][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.862][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:05:54.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:05:54.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:05:54.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:05:54.901][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-03-29 16:05:54.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:05:54.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:05:54.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:05:54.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:05:54.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:05:54.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:05:54.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:05:54.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:05:54.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:05:54.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:05:54.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:54.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:05:54.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:05:54.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:54.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:05:54.932][biodb::testThat]
biodb.INFO [2025-03-29 16:05:54.932][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-29 16:05:54.933][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:54.934][biodb::testThat]
biodb.INFO [2025-03-29 16:05:54.939][biodb::testThat]
biodb.INFO [2025-03-29 16:05:54.940][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-29 16:05:54.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:54.942][biodb::testThat]
biodb.WARN [2025-03-29 16:05:54.959][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-29 16:05:54.976][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-29 16:05:54.984][biodb::testThat]
biodb.INFO [2025-03-29 16:05:54.984][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-29 16:05:54.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:54.986][biodb::testThat]
biodb.TRACE[2025-03-29 16:05:55.010][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:05:55.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:05:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:55.013][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:05:55.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:05:55.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:55.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:55.017][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:05:55.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:05:55.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:55.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:55.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:05:55.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:05:55.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:55.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:55.053][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:05:55.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:05:55.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:55.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:55.057][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:05:55.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:05:55.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:55.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:55.060][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:05:55.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:05:55.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:55.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:05:55.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:05:55.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:05:55.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:05:55.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:05:55.072][biodb::testThat]
biodb.INFO [2025-03-29 16:05:55.072][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-29 16:05:55.073][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:55.074][biodb::testThat]
biodb.INFO [2025-03-29 16:05:55.080][biodb::testThat]
biodb.INFO [2025-03-29 16:05:55.081][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-29 16:05:55.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:55.083][biodb::testThat]
biodb.INFO [2025-03-29 16:05:55.088][biodb::testThat]
biodb.INFO [2025-03-29 16:05:55.089][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-29 16:05:55.090][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:55.091][biodb::testThat]
biodb.INFO [2025-03-29 16:05:55.096][biodb::testThat]
biodb.INFO [2025-03-29 16:05:55.097][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-29 16:05:55.097][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:05:55.098][biodb::testThat]
biodb.INFO [2025-03-29 16:05:55.103][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:05:55.104][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-29 16:05:55.105][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-29 16:05:55.106][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:05:55.106][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.108][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.110][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.110][FUN] Functions in observer BiodbConfig: [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 [2025-03-29 16:05:55.122][biodb::testContext]
biodb.INFO [2025-03-29 16:05:55.123][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:05:55.124][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-29 16:05:55.124][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:05:55.125][biodb::testContext]
biodb.INFO [2025-03-29 16:05:55.127][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:05:55.128][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:05:55.132][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:05:55.133][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:05:55.134][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:05:55.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.137][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:05:55.138][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:05:55.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.141][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:05:55.142][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:05:55.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.145][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:05:55.146][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:05:55.147][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:05:55.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.150][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:05:55.151][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:05:55.152][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:05:55.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.155][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:05:55.156][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:05:55.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.159][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:05:55.160][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:05:55.161][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:05:55.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.164][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:05:55.165][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:05:55.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.168][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:05:55.169][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:05:55.170][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:05:55.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.173][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:05:55.174][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:05:55.175][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:05:55.176][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:05:55.177][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:05:55.178][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:05:55.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.181][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:05:55.182][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:05:55.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.185][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:05:55.186][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:05:55.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.189][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:05:55.190][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:05:55.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.193][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:05:55.194][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:05:55.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.197][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:05:55.198][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:05:55.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.201][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:05:55.202][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:05:55.205][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:05:55.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.208][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:05:55.209][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:05:55.210][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:05:55.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.214][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:05:55.215][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.216][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-29 16:05:55.217][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.218][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:55.219][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.220][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.220][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.221][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.222][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:05:55.223][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:55.224][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.225][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:05:55.226][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:55.227][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.227][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.228][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:05:55.228][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:05:55.228][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:05:55.228][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:05:55.228][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:05:55.229][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:05:55.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.232][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:55.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.234][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.235][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.236][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:55.237][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:55.238][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.238][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.239][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:05:55.241][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.245][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:05:55.246][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.247][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:55.248][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.249][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.249][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.250][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.251][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:05:55.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:55.253][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.254][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:05:55.255][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:55.256][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.257][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:05:55.257][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:05:55.257][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:05:55.257][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:05:55.257][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:05:55.258][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:05:55.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:55.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.263][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.264][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.265][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:55.266][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:55.266][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.267][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.268][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:05:55.270][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.271][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-29 16:05:55.272][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.273][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:55.273][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.274][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.275][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.276][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.277][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:05:55.278][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:55.279][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.280][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:05:55.280][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:55.281][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.282][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.283][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.284][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:05:55.285][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.286][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.286][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:55.287][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.289][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.290][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.291][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:55.291][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:55.292][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.293][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.294][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:05:55.296][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.297][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:05:55.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:55.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.300][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.301][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.302][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.303][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:05:55.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:55.304][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.305][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:05:55.306][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:55.307][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.308][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.309][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.310][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:05:55.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:55.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.316][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:55.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:55.318][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.319][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.320][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:05:55.321][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.326][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[2025-03-29 16:05:55.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.337][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[2025-03-29 16:05:55.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.349][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[2025-03-29 16:05:55.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.391][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:05:55.393][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:05:55.394][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:05:55.395][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:05:55.396][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:05:55.398][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:05:55.399][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:05:55.400][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:05:55.401][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:05:55.403][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:05:55.404][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:05:55.405][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:05:55.406][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:05:55.407][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:05:55.409][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:05:55.410][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:05:55.411][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:05:55.412][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:05:55.413][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:05:55.415][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:05:55.416][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:05:55.417][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:05:55.418][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:05:55.420][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:05:55.421][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:05:55.422][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:05:55.423][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:05:55.425][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:05:55.426][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:05:55.427][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:05:55.428][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:05:55.429][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:05:55.431][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:05:55.432][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:05:55.433][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:05:55.434][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:05:55.435][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:05:55.437][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:05:55.438][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:05:55.439][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:05:55.440][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:05:55.442][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:05:55.443][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:05:55.444][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:05:55.445][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:05:55.446][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:05:55.448][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:05:55.449][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:05:55.450][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:05:55.451][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:05:55.453][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:05:55.454][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:05:55.455][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:05:55.456][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:05:55.457][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:05:55.459][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:05:55.460][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:05:55.461][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:05:55.462][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:05:55.464][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:05:55.465][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:05:55.466][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:05:55.467][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:05:55.468][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:05:55.470][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:05:55.471][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:05:55.472][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:05:55.473][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:05:55.475][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:05:55.476][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:05:55.477][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:05:55.481][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:05:55.482][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:05:55.484][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:05:55.485][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:05:55.486][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:05:55.487][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:05:55.488][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:05:55.490][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:05:55.491][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:05:55.492][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:05:55.493][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:05:55.495][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:05:55.496][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:05:55.497][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:05:55.498][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:05:55.499][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.500][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:05:55.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:05:55.597][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-29 16:05:55.598][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-29 16:05:55.600][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.601][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-29 16:05:55.602][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.603][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:05:55.603][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.604][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-29 16:05:55.605][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.606][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.607][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-29 16:05:55.608][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:05:55.609][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.609][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-29 16:05:55.610][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:05:55.611][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-29 16:05:55.611][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-29 16:05:55.611][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-29 16:05:55.611][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-29 16:05:55.611][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-29 16:05:55.611][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-29 16:05:55.611][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-29 16:05:55.612][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:05:55.613][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.614][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:05:55.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.616][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:05:55.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:05:55.618][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:05:55.619][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:05:55.620][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-29 16:05:55.620][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-29 16:05:55.620][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-29 16:05:55.620][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-29 16:05:55.621][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:05:55.621][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:05:55.622][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:05:55.623][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:05:55.624][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-29 16:05:55.627][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-29 16:05:55.628][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-29 16:05:55.629][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-29 16:05:55.630][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-29 16:05:55.631][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:05:55.632][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:05:55.633][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:05:55.634][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:05:55.635][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:05:55.636][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-29 16:05:55.637][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:05:55.638][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-29 16:05:55.639][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-29 16:05:55.640][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:05:55.640][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:05:55.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:05:55.642][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:05:55.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:05:55.643][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:05:55.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  4.053   0.162   4.205

'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)