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 merida1

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

raw results


Summary

Package: biodbNci
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.10.0.tar.gz
StartedAt: 2025-03-29 16:02:19 -0400 (Sat, 29 Mar 2025)
EndedAt: 2025-03-29 16:03:33 -0400 (Sat, 29 Mar 2025)
EllapsedTime: 74.0 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-apple-darwin20

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-03-29 16:03:28.932][biodb::testContext]
biodb.INFO [2025-03-29 16:03:28.935][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:03:28.936][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-29 16:03:28.938][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:03:28.939][biodb::testContext]
biodb.INFO [2025-03-29 16:03:28.945][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:03:28.947][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:03:28.954][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:28.956][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:03:28.957][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:03:28.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:28.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:28.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:28.962][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:03:28.987][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:03:28.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:28.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:28.990][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:28.991][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:03:28.993][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:03:28.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:28.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:28.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:28.997][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:03:28.998][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:03:29.000][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:03:29.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.004][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:03:29.005][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:03:29.007][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:03:29.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.011][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:03:29.013][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:03:29.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.017][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:03:29.018][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:03:29.020][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:03:29.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.024][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:03:29.025][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:03:29.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.030][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:03:29.031][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:03:29.032][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:03:29.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.037][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:03:29.038][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:03:29.040][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:03:29.041][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:03:29.042][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:03:29.044][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:03:29.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.047][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.048][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:03:29.049][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:03:29.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.054][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:03:29.055][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:03:29.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.058][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.060][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:03:29.061][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:03:29.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.065][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:03:29.067][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:03:29.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.070][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.071][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:03:29.072][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:03:29.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.077][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:03:29.078][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:03:29.089][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:03:29.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.093][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 16:03:29.094][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:03:29.096][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:03:29.097][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:03:29.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.104][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:03:29.149][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.176][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-29 16:03:29.177][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.178][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:29.180][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.181][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.182][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.183][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.185][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:03:29.186][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:29.187][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.188][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:03:29.189][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:29.191][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.192][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.193][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:29.193][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:03:29.193][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:03:29.193][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:03:29.193][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:03:29.195][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:29.196][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.198][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:29.199][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.200][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.201][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.203][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.204][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:29.205][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:29.206][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.207][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.209][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:03:29.211][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.212][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:03:29.214][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.215][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:29.216][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.217][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.218][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.220][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.221][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:03:29.222][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:29.224][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.225][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:03:29.226][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:29.227][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.228][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.230][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:29.230][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:03:29.230][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:03:29.230][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:03:29.230][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:03:29.231][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:29.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.235][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:29.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.237][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.238][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.239][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.241][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:29.242][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:29.243][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.244][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.246][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:03:29.248][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.249][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-29 16:03:29.250][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:29.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.254][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.255][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.258][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:03:29.259][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:29.260][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.262][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:03:29.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:29.264][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.265][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.266][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.268][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:29.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.271][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:29.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.275][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.276][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.277][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:29.278][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:29.280][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.281][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.282][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:03:29.284][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.286][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:03:29.287][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:29.289][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.291][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.292][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.293][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.294][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:03:29.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:29.297][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.298][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:03:29.299][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:29.301][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.302][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.303][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.304][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:29.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.308][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:29.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.311][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.313][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.314][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:29.315][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:29.316][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.318][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.321][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:29.323][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.324][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.327][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 16:03:29.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.329][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 16:03:29.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.333][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 16:03:29.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.335][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.338][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 16:03:29.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.340][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.344][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 16:03:29.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.346][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 16:03:29.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.349][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 16:03:29.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.351][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.355][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 16:03:29.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.357][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 16:03:29.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.360][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 16:03:29.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.362][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.366][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 16:03:29.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.368][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.371][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 16:03:29.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.373][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.376][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 16:03:29.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.379][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 16:03:29.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.386][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 16:03:29.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.388][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:29.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.394][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.397][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 16:03:29.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.399][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:29.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.408][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 16:03:29.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.410][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.413][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 16:03:29.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.415][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:29.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.421][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.422][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:03:29.426][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:03:29.428][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:03:29.430][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:03:29.432][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:03:29.433][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:03:29.435][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:03:29.437][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:03:29.439][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:03:29.441][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:03:29.442][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:03:29.444][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:03:29.446][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:03:29.448][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:03:29.449][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:03:29.451][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:03:29.453][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:03:29.454][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:03:29.456][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:03:29.458][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:03:29.460][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:03:29.461][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:03:29.463][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:03:29.465][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:03:29.467][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:03:29.469][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:03:29.470][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:03:29.472][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:03:29.474][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:03:29.476][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:03:29.478][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:03:29.479][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:03:29.481][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:03:29.483][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:03:29.484][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:03:29.486][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:03:29.488][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:03:29.490][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:03:29.491][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:03:29.493][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:03:29.495][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:03:29.497][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:03:29.498][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:03:29.500][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:03:29.502][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:03:29.504][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:03:29.506][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:03:29.507][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:03:29.509][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:03:29.511][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:03:29.513][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:03:29.515][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:03:29.516][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:03:29.518][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:03:29.520][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:03:29.522][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:03:29.523][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:03:29.525][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:03:29.527][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:03:29.529][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:03:29.530][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:03:29.532][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:03:29.534][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:03:29.536][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:03:29.537][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:03:29.539][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:03:29.541][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:03:29.543][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:03:29.544][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:03:29.546][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:03:29.548][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:03:29.549][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:03:29.551][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:03:29.553][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:03:29.555][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:03:29.556][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:03:29.558][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:03:29.560][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:03:29.562][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:03:29.563][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:03:29.565][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:03:29.567][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:03:29.569][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:03:29.576][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:03:29.578][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:03:29.582][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:29.583][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.584][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 16:03:29.585][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.586][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.597][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 16:03:29.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.599][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.610][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 16:03:29.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.613][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.618][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 16:03:29.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.620][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.626][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 16:03:29.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.628][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.633][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 16:03:29.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.635][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.641][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 16:03:29.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.643][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.649][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 16:03:29.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.651][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.656][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 16:03:29.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.658][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.664][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 16:03:29.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.666][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.672][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 16:03:29.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.674][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.680][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 16:03:29.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.682][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.687][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 16:03:29.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.690][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:29.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:29.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.703][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 16:03:29.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.705][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.710][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 16:03:29.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.712][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.718][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 16:03:29.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.720][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:29.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.726][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 16:03:29.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.728][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:29.731][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-29 16:03:29.743][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-29 16:03:29.746][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.747][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-29 16:03:29.748][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:29.751][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.752][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-29 16:03:29.753][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.755][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-29 16:03:29.757][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:29.758][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.759][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-29 16:03:29.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:29.761][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-29 16:03:29.761][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-29 16:03:29.761][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-29 16:03:29.761][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-29 16:03:29.761][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-29 16:03:29.761][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-29 16:03:29.761][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-29 16:03:29.763][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:29.764][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.765][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:03:29.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.769][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:29.770][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:29.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:29.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:29.773][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-29 16:03:29.773][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-29 16:03:29.773][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-29 16:03:29.773][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-29 16:03:29.774][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:29.775][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:29.777][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:29.778][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:29.786][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-29 16:03:29.807][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-29 16:03:29.809][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-29 16:03:29.813][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-29 16:03:29.817][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-29 16:03:29.822][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:03:29.823][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:03:29.825][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:03:29.826][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:03:29.828][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:03:29.857][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-29 16:03:29.867][biodb::testThat]
biodb.INFO [2025-03-29 16:03:29.868][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-29 16:03:29.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:29.871][biodb::testThat]
biodb.TRACE[2025-03-29 16:03:29.875][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-03-29 16:03:29.877][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:03:29.881][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-29 16:03:29.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:29.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:29.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:29.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:29.908][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 16:03:29.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:29.910][FUN] Functions in observer BiodbConfig: [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 16:03:29.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:29.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:29.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:29.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:29.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:29.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:29.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:29.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:29.960][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:29.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:29.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:29.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.001][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.041][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.046][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.056][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:30.143][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-03-29 16:03:30.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:30.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:30.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.150][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:30.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:30.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.155][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:30.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:30.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.160][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:30.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:30.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.203][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.245][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.250][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.260][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.288][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.289][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.307][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.317][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.322][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.323][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.327][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.357][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.358][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.392][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.394][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.396][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.427][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.428][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.452][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.453][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.462][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.463][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.466][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.472][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.473][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.476][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.482][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.483][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.486][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.492][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.493][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.519][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-03-29 16:03:30.567][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:03:30.569][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-29 16:03:30.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:30.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:30.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:30.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:30.581][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 16:03:30.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:30.584][FUN] Functions in observer BiodbConfig: [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 16:03:30.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.640][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.645][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.651][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:30.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:30.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:30.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:30.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:30.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:30.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:30.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:30.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:30.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:30.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:30.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:30.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:30.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:30.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:30.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:30.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:30.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.708][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:30.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:30.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:30.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.729][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.734][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.744][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:30.779][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-03-29 16:03:30.806][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:30.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:30.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.815][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:30.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:30.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:30.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:30.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:30.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:30.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.874][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.916][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.921][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.926][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:30.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.966][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.970][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:30.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:30.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.985][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.990][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:30.995][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:30.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:30.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.000][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.001][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.003][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.004][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.038][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.039][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.057][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.072][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.073][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.076][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.077][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.106][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.107][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.110][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.141][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.142][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.176][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.177][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.195][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.197][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.205][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.207][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.213][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.219][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.220][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.229][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.230][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.238][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.239][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.248][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.249][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.258][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.261][ef$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:31.271][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.272][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-29 16:03:31.273][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:31.274][biodb::testThat]
biodb.DEBUG[2025-03-29 16:03:31.277][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-03-29 16:03:31.284][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-03-29 16:03:31.288][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:31.290][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-03-29 16:03:31.292][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-03-29 16:03:31.294][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-03-29 16:03:31.296][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-03-29 16:03:31.298][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-29 16:03:31.299][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-03-29 16:03:31.300][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-03-29 16:03:31.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:31.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:31.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:31.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:31.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:31.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:03:31.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.379][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.384][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.393][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:31.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:03:31.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:31.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:31.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:31.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:31.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:03:31.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.456][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.461][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:03:31.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.466][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:03:31.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:03:31.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-29 16:03:31.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.516][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:31.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:31.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:03:31.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:03:31.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:03:31.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.548][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.558][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-29 16:03:31.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:03:31.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:03:31.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:31.611][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-03-29 16:03:31.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:03:31.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:03:31.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:03:31.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:03:31.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:03:31.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:03:31.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:03:31.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:03:31.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:03:31.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:03:31.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:03:31.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:03:31.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:31.657][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.658][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-29 16:03:31.659][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:31.660][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.668][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.670][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-29 16:03:31.671][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:31.672][biodb::testThat]
biodb.WARN [2025-03-29 16:03:31.698][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-29 16:03:31.723][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-29 16:03:31.734][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.735][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-29 16:03:31.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:31.737][biodb::testThat]
biodb.TRACE[2025-03-29 16:03:31.772][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:31.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:31.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.777][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:31.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:31.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.782][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:31.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:31.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.787][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:31.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:31.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.837][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:31.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:31.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.843][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:31.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:31.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.848][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:31.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:31.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:31.854][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:31.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:31.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:31.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:31.867][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.868][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-29 16:03:31.869][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:31.870][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.880][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.881][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-29 16:03:31.883][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:31.884][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.894][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.896][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-29 16:03:31.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:31.898][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.907][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.908][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-29 16:03:31.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:31.910][biodb::testThat]
biodb.INFO [2025-03-29 16:03:31.919][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:03:31.920][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-29 16:03:31.922][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-29 16:03:31.923][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:03:31.924][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:31.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:31.926][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:31.927][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 16:03:31.928][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.929][FUN] Functions in observer BiodbConfig: [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 16:03:31.947][biodb::testContext]
biodb.INFO [2025-03-29 16:03:31.948][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:03:31.949][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-29 16:03:31.950][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:03:31.952][biodb::testContext]
biodb.INFO [2025-03-29 16:03:31.954][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:03:31.956][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:03:31.960][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:31.961][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:03:31.963][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:03:31.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:31.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:31.967][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:03:31.969][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:03:31.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:31.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.972][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:31.973][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:03:31.974][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:03:31.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:31.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:31.979][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:03:31.980][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:03:31.981][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:03:31.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:31.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.985][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:31.986][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:03:31.987][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:03:31.988][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:03:31.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:31.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:31.993][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:03:31.994][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:03:31.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:31.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:31.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:31.999][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:03:32.000][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:03:32.001][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:03:32.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.006][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:03:32.007][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:03:32.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.010][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.012][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:03:32.013][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:03:32.014][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:03:32.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.019][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:03:32.020][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:03:32.021][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:03:32.022][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:03:32.024][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:03:32.025][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:03:32.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.028][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.029][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:03:32.031][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:03:32.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.035][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:03:32.037][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:03:32.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.040][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.041][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:03:32.043][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:03:32.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.047][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:03:32.049][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:03:32.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.052][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.053][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:03:32.055][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:03:32.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.059][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:03:32.060][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:03:32.071][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:03:32.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.076][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:03:32.077][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:03:32.079][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:03:32.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.084][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:03:32.086][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.087][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-29 16:03:32.088][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:32.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.095][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.096][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:03:32.097][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:32.099][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.100][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:03:32.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:32.103][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.104][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.105][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:32.105][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:03:32.105][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:03:32.105][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:03:32.105][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:03:32.106][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:32.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.110][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:32.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.115][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.116][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:32.117][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:32.123][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.125][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.126][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:03:32.128][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.130][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:03:32.131][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.132][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:32.133][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.135][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.136][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.137][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.138][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:03:32.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:32.141][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.142][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:03:32.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:32.144][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.146][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.147][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:03:32.147][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:03:32.147][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:03:32.147][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:03:32.147][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:03:32.148][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:32.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.152][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:32.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.155][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.156][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.157][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:32.159][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:32.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.161][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.162][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:03:32.165][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.166][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-29 16:03:32.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:32.170][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.171][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.172][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.174][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:03:32.176][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:32.177][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.178][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:03:32.179][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:32.181][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.182][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.183][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.184][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:32.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.188][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:32.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.191][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.192][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.194][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:32.195][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:32.196][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.197][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.199][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:03:32.201][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.202][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:03:32.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.204][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:32.206][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.207][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.208][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.209][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.211][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:03:32.212][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:32.213][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.214][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:03:32.216][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:32.217][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.218][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.219][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.220][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:03:32.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.223][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.224][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:32.225][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.227][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.229][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.230][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:32.231][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:32.232][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.233][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.235][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:32.236][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.237][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.240][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 16:03:32.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.243][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.246][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 16:03:32.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.248][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.254][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.259][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.262][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 16:03:32.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.265][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.268][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 16:03:32.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.270][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.273][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 16:03:32.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.275][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.279][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 16:03:32.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.281][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.284][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 16:03:32.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.290][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.294][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 16:03:32.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.296][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 16:03:32.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.307][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 16:03:32.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.310][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 16:03:32.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.312][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.316][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 16:03:32.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.318][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.321][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 16:03:32.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.323][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 16:03:32.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.327][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 16:03:32.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.329][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 16:03:32.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.332][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 16:03:32.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.334][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 16:03:32.336][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:03:32.337][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:03:32.339][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:03:32.341][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:03:32.342][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:03:32.344][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:03:32.346][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:03:32.347][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:03:32.349][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:03:32.351][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:03:32.353][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:03:32.354][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:03:32.356][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:03:32.358][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:03:32.359][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:03:32.361][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:03:32.363][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:03:32.365][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:03:32.366][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:03:32.368][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:03:32.370][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:03:32.371][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:03:32.373][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:03:32.375][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:03:32.376][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:03:32.378][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:03:32.380][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:03:32.382][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:03:32.383][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:03:32.385][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:03:32.387][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:03:32.388][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:03:32.390][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:03:32.392][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:03:32.393][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:03:32.395][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:03:32.397][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:03:32.399][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:03:32.400][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:03:32.402][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:03:32.404][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:03:32.405][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:03:32.407][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:03:32.409][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:03:32.410][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:03:32.412][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:03:32.414][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:03:32.416][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:03:32.417][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:03:32.419][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:03:32.421][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:03:32.422][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:03:32.424][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:03:32.426][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:03:32.427][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:03:32.429][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:03:32.431][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:03:32.433][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:03:32.434][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:03:32.436][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:03:32.438][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:03:32.439][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:03:32.441][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:03:32.443][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:03:32.444][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:03:32.446][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:03:32.448][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:03:32.455][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:03:32.456][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:03:32.458][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:03:32.460][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:03:32.462][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:03:32.463][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:03:32.465][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:03:32.467][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:03:32.469][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:03:32.471][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:03:32.473][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:03:32.474][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:03:32.476][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:03:32.478][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:03:32.479][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:03:32.481][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:03:32.483][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:03:32.485][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:03:32.486][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:03:32.487][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.489][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.490][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.506][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.519][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 16:03:32.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.521][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.527][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 16:03:32.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.529][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.534][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 16:03:32.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.536][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.542][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 16:03:32.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.544][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 16:03:32.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.550][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 16:03:32.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.552][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.558][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 16:03:32.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.560][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.565][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 16:03:32.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.567][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.573][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 16:03:32.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.575][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:32.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.588][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 16:03:32.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.590][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.596][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 16:03:32.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.598][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.603][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 16:03:32.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.606][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.611][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 16:03:32.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.613][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:03:32.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:03:32.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.623][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 16:03:32.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:03:32.628][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-29 16:03:32.630][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-29 16:03:32.632][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.633][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-29 16:03:32.635][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.636][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:03:32.637][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.638][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-29 16:03:32.639][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.642][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-29 16:03:32.643][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:03:32.644][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.646][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-29 16:03:32.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:03:32.648][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-29 16:03:32.648][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-29 16:03:32.648][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-29 16:03:32.648][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-29 16:03:32.648][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-29 16:03:32.648][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-29 16:03:32.648][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-29 16:03:32.649][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:03:32.651][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.652][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:03:32.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.655][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:03:32.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:03:32.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:03:32.659][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:03:32.660][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-29 16:03:32.660][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-29 16:03:32.660][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-29 16:03:32.660][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-29 16:03:32.661][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:03:32.662][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:03:32.663][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:03:32.665][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:03:32.672][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-29 16:03:32.676][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-29 16:03:32.677][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-29 16:03:32.679][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-29 16:03:32.681][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-29 16:03:32.682][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:03:32.683][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:03:32.685][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:03:32.686][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:03:32.688][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-29 16:03:32.689][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-29 16:03:32.690][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:03:32.691][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-29 16:03:32.693][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-29 16:03:32.694][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:03:32.695][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:32.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:32.697][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:32.698][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 16:03:32.699][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:32.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  5.682   0.322   6.022

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.10.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-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)